Esempio n. 1
0
 public MatrixZoomData getControlZd() {
   Matrix matrix = getControlMatrix();
   if (matrix == null || currentZoom == null) {
     return null;
   } else {
     return matrix.getZoomData(currentZoom);
   }
 }
Esempio n. 2
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 public MatrixZoomData getZd() throws UninitializedObjectException {
   Matrix matrix = getMatrix();
   if (matrix == null) {
     throw new UninitializedObjectException("Uninitialized matrix");
   } else if (currentZoom == null) {
     throw new UninitializedObjectException("Uninitialized zoom");
   } else {
     return matrix.getZoomData(currentZoom);
   }
 }
Esempio n. 3
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 public void applyMatricesToVertices(MDL mdlr) {
   int sz = numVerteces();
   for (int i = 0; i < sz; i++) {
     GeosetVertex gv = vertex.get(i);
     gv.clearBoneAttachments();
     Matrix mx = getMatrix(gv.getVertexGroup());
     mx.updateIds(mdlr);
     int szmx = mx.size();
     for (int m = 0; m < szmx; m++) {
       gv.addBoneAttachment((Bone) mdlr.getIdObject(mx.getBoneId(m)));
     }
   }
 }
Esempio n. 4
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 public void applyVerticesToMatrices(MDL mdlr) {
   matrix.clear();
   for (int i = 0; i < vertex.size(); i++) {
     Matrix newTemp = new Matrix(vertex.get(i).bones);
     boolean newMatrix = true;
     for (int m = 0; m < matrix.size() && newMatrix; m++) {
       if (newTemp.equals(matrix.get(m))) {
         newTemp = matrix.get(m);
         newMatrix = false;
       }
     }
     if (newMatrix) {
       matrix.add(newTemp);
       newTemp.updateIds(mdlr);
     }
     vertex.get(i).VertexGroup = matrix.indexOf(newTemp);
     vertex.get(i).setMatrix(newTemp);
   }
 }
Esempio n. 5
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  private void unsafeSave1DTrackToWigFile(
      Chromosome chromosomeForPosition, PrintWriter printWriter, int binStartPosition)
      throws IOException {
    int resolution = getZoom().getBinSize();
    for (Chromosome chromosome : chromosomes) {
      if (chromosome.getName().equals(Globals.CHR_ALL)) continue;
      Matrix matrix = null;
      if (displayOption == MatrixType.OBSERVED) {
        matrix = dataset.getMatrix(chromosomeForPosition, chromosome);
      } else if (displayOption == MatrixType.CONTROL) {
        matrix = controlDataset.getMatrix(chromosomeForPosition, chromosome);
      }

      if (matrix == null) continue;

      MatrixZoomData zd = matrix.getZoomData(currentZoom);
      printWriter.println(
          "fixedStep chrom=chr"
              + chromosome.getName().replace("chr", "")
              + " start=1 step="
              + resolution
              + " span="
              + resolution);

      int[] regionIndices;
      if (chromosomeForPosition.getIndex() < chromosome.getIndex()) {
        regionIndices = new int[] {binStartPosition, binStartPosition, 0, chromosome.getLength()};
      } else {
        regionIndices = new int[] {0, chromosome.getLength(), binStartPosition, binStartPosition};
      }

      zd.dump1DTrackFromCrossHairAsWig(
          printWriter,
          chromosomeForPosition,
          binStartPosition,
          chromosomeForPosition.getIndex() == chromosome.getIndex(),
          regionIndices,
          normalizationType,
          displayOption,
          getExpectedValues());
    }
  }
 public static void main(String[] args) throws Exception {
   fw = new FileWriter("/Users/Main/Desktop/test.csv", false); // ※1
   pw = new PrintWriter(new BufferedWriter(fw));
   for (range = 1; range < 1000000; range *= 2) {
     for (int j = 0; j < 3; j++) {
       for (int i = 0; i < 1; i++) {
         Vector X = Vector.generate(n, range);
         Matrix A = Matrix.generate(n, n, range);
         Vector B = A.multi(X);
         pw.print(range);
         pw.print(",");
         pw.print(n);
         System.out.println(n);
         analysisGaussianEliminationWithPivot(A, B, X);
         System.out.println();
       }
     }
   }
   pw.close();
 }
Esempio n. 7
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 public void updateToObjects(MDL mdlr) {
   // upload the temporary UVLayer and Matrix objects into the vertices themselves
   int sz = numVerteces();
   for (Matrix m : matrix) {
     m.updateBones(mdlr);
   }
   for (int i = 0; i < sz; i++) {
     GeosetVertex gv = vertex.get(i);
     gv.clearTVerts();
     int szuv = uvlayers.size();
     for (int l = 0; l < szuv; l++) {
       try {
         gv.addTVertex(uvlayers.get(l).getTVertex(i));
       } catch (Exception e) {
         JOptionPane.showMessageDialog(
             MDLReader.getDefaultContainer(),
             "Error: Length of TVertices and Vertices chunk differ (Or some other unknown error has occurred)!");
       }
     }
     Matrix mx = getMatrix(gv.getVertexGroup());
     int szmx = mx.size();
     gv.clearBoneAttachments();
     for (int m = 0; m < szmx; m++) {
       gv.addBoneAttachment((Bone) mdlr.getIdObject(mx.getBoneId(m)));
     }
     gv.setNormal(normals.get(i));
     for (Triangle t : triangle) {
       if (t.containsRef(gv)) {
         gv.triangles.add(t);
       }
     }
     gv.geoset = this;
     //             gv.addBoneAttachment(null);//Why was this here?
   }
   try {
     material = mdlr.getMaterial(materialID);
   } catch (ArrayIndexOutOfBoundsException e) {
     JOptionPane.showMessageDialog(null, "Error: Material index out of bounds for geoset!");
   }
   parentModel = mdlr;
 }
Esempio n. 8
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  /**
   * Compute the bounding screen extent of a rotated rectangle.
   *
   * @param rect Rectangle to rotate.
   * @param x X coordinate of the rotation point.
   * @param y Y coordinate of the rotation point.
   * @param rotation Rotation angle.
   * @return The smallest rectangle that completely contains {@code rect} when rotated by the
   *     specified angle.
   */
  protected Rectangle computeRotatedScreenExtent(Rectangle rect, int x, int y, Angle rotation) {
    Rectangle r = new Rectangle(rect);

    // Translate the rectangle to the rotation point.
    r.translate(-x, -y);

    // Compute corner points
    Vec4[] corners = {
      new Vec4(r.getMaxX(), r.getMaxY()),
      new Vec4(r.getMaxX(), r.getMinY()),
      new Vec4(r.getMinX(), r.getMaxY()),
      new Vec4(r.getMinX(), r.getMinY())
    };

    // Rotate the rectangle
    Matrix rotationMatrix = Matrix.fromRotationZ(rotation);
    for (int i = 0; i < corners.length; i++) {
      corners[i] = corners[i].transformBy3(rotationMatrix);
    }

    // Find the bounding rectangle of rotated points.
    int minX = Integer.MAX_VALUE;
    int minY = Integer.MAX_VALUE;
    int maxX = -Integer.MAX_VALUE;
    int maxY = -Integer.MAX_VALUE;

    for (Vec4 v : corners) {
      if (v.x > maxX) maxX = (int) v.x;

      if (v.x < minX) minX = (int) v.x;

      if (v.y > maxY) maxY = (int) v.y;

      if (v.y < minY) minY = (int) v.y;
    }

    // Set bounds and translate the rectangle back to where it started.
    r.setBounds(minX, minY, maxX - minX, maxY - minY);
    r.translate(x, y);

    return r;
  }
 public static void analysisGaussianEliminationWithPivot(Matrix A, Vector B, Vector X) {
   System.out.println("GaussianElimination");
   pw.print(",");
   pw.print("GaussianElimination");
   analysis(
       X,
       () -> {
         try {
           return Algorithm.gaussianEliminationWithPivot(A.toDoubleArray(), B.toDoubleArray());
         } catch (Exception e) {
           e.printStackTrace();
           pw.print(",");
           pw.print("-");
           pw.print(",");
           pw.print("-");
           pw.println();
           return new double[0];
         }
       });
 }
Esempio n. 10
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  public void doSavePrep(MDL mdlr) {
    purifyFaces();

    // Normals cleared here, in case that becomes a problem later.
    normals.clear();
    // UV Layers cleared here
    uvlayers.clear();
    int bigNum = 0;
    int littleNum = -1;
    for (int i = 0; i < vertex.size(); i++) {
      int temp = vertex.get(i).tverts.size();
      if (temp > bigNum) {
        bigNum = temp;
      }
      if (littleNum == -1 || temp < littleNum) {
        littleNum = temp;
      }
    }
    if (littleNum != bigNum) {
      JOptionPane.showMessageDialog(
          null,
          "Error: Attempting to save a Geoset with Verteces that have differing numbers of TVertices! Empty TVertices will be autogenerated.");
    }
    for (int i = 0; i < bigNum; i++) {
      uvlayers.add(new UVLayer());
    }
    for (int i = 0; i < vertex.size(); i++) {
      normals.add(vertex.get(i).getNormal());
      for (int uv = 0; uv < bigNum; uv++) {
        TVertex temp = vertex.get(i).getTVertex(uv);
        if (temp != null) {
          uvlayers.get(uv).addTVertex(temp);
        } else {
          uvlayers.get(uv).addTVertex(new TVertex(0, 0));
        }
      }
    }
    // Clearing matrix list
    matrix.clear();
    for (int i = 0; i < vertex.size(); i++) {
      Matrix newTemp = new Matrix(vertex.get(i).bones);
      boolean newMatrix = true;
      for (int m = 0; m < matrix.size() && newMatrix; m++) {
        if (newTemp.equals(matrix.get(m))) {
          newTemp = matrix.get(m);
          newMatrix = false;
        }
      }
      if (newMatrix) {
        matrix.add(newTemp);
        newTemp.updateIds(mdlr);
      }
      vertex.get(i).VertexGroup = matrix.indexOf(newTemp);
      vertex.get(i).setMatrix(newTemp);
    }
    for (int i = 0; i < triangle.size(); i++) {
      triangle.get(i).updateVertexIds(this);
    }
    int boneRefCount = 0;
    for (int i = 0; i < matrix.size(); i++) {
      boneRefCount += matrix.get(i).bones.size();
    }
    for (int i = 0; i < matrix.size(); i++) {
      matrix.get(i).updateIds(mdlr);
    }
  }
Esempio n. 11
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  public void printTo(PrintWriter writer, MDL mdlr, boolean trianglesTogether) {
    purifyFaces();
    writer.println("Geoset {");
    writer.println("\tVertices " + vertex.size() + " {");

    String tabs = "\t\t";
    // Normals cleared here, in case that becomes a problem later.
    normals.clear();
    // UV Layers cleared here
    uvlayers.clear();
    int bigNum = 0;
    int littleNum = -1;
    for (int i = 0; i < vertex.size(); i++) {
      int temp = vertex.get(i).tverts.size();
      if (temp > bigNum) {
        bigNum = temp;
      }
      if (littleNum == -1 || temp < littleNum) {
        littleNum = temp;
      }
    }
    if (littleNum != bigNum) {
      JOptionPane.showMessageDialog(
          null,
          "Error: Attempting to save a Geoset with Verteces that have differing numbers of TVertices! Empty TVertices will be autogenerated.");
    }
    for (int i = 0; i < bigNum; i++) {
      uvlayers.add(new UVLayer());
    }
    for (int i = 0; i < vertex.size(); i++) {
      writer.println(tabs + vertex.get(i).toString() + ",");
      normals.add(vertex.get(i).getNormal());
      for (int uv = 0; uv < bigNum; uv++) {
        try {
          TVertex temp = vertex.get(i).getTVertex(uv);
          if (temp != null) {
            uvlayers.get(uv).addTVertex(temp);
          } else {
            uvlayers.get(uv).addTVertex(new TVertex(0, 0));
          }
        } catch (IndexOutOfBoundsException e) {
          uvlayers.get(uv).addTVertex(new TVertex(0, 0));
        }
      }
    }
    writer.println("\t}");
    writer.println("\tNormals " + normals.size() + " {");
    for (int i = 0; i < normals.size(); i++) {
      writer.println(tabs + normals.get(i).toString() + ",");
    }
    writer.println("\t}");
    for (int i = 0; i < uvlayers.size(); i++) {
      uvlayers.get(i).printTo(writer, 1, true);
    }
    // Clearing matrix list
    matrix.clear();
    writer.println("\tVertexGroup {");
    for (int i = 0; i < vertex.size(); i++) {
      Matrix newTemp = new Matrix(vertex.get(i).bones);
      boolean newMatrix = true;
      for (int m = 0; m < matrix.size() && newMatrix; m++) {
        if (newTemp.equals(matrix.get(m))) {
          newTemp = matrix.get(m);
          newMatrix = false;
        }
      }
      if (newMatrix) {
        matrix.add(newTemp);
        newTemp.updateIds(mdlr);
      }
      vertex.get(i).VertexGroup = matrix.indexOf(newTemp);
      vertex.get(i).setMatrix(newTemp);
      writer.println(tabs + vertex.get(i).VertexGroup + ",");
    }
    writer.println("\t}");
    if (trianglesTogether) {
      writer.println("\tFaces 1 " + (triangle.size() * 3) + " {");
      writer.println("\t\tTriangles {");
      String triangleOut = "\t\t\t{ ";
      for (int i = 0; i < triangle.size(); i++) {
        triangle.get(i).updateVertexIds(this);
        if (i != triangle.size() - 1) {
          triangleOut = triangleOut + triangle.get(i).toString() + ", ";
        } else {
          triangleOut = triangleOut + triangle.get(i).toString() + " ";
        }
      }
      writer.println(triangleOut + "},");
      writer.println("\t\t}");
    } else {
      writer.println("\tFaces " + triangle.size() + " " + (triangle.size() * 3) + " {");
      writer.println("\t\tTriangles {");
      String triangleOut = "\t\t\t{ ";
      for (int i = 0; i < triangle.size(); i++) {
        triangle.get(i).updateVertexIds(this);
        writer.println(triangleOut + triangle.get(i).toString() + " },");
      }
      writer.println("\t\t}");
    }
    writer.println("\t}");
    int boneRefCount = 0;
    for (int i = 0; i < matrix.size(); i++) {
      boneRefCount += matrix.get(i).bones.size();
    }
    writer.println("\tGroups " + matrix.size() + " " + boneRefCount + " {");
    for (int i = 0; i < matrix.size(); i++) {
      matrix.get(i).updateIds(mdlr);
      matrix.get(i).printTo(writer, 2); // 2 is the tab height
    }
    writer.println("\t}");
    if (extents != null) extents.printTo(writer, 1);
    for (int i = 0; i < anims.size(); i++) {
      anims.get(i).printTo(writer, 1);
    }

    writer.println("\tMaterialID " + materialID + ",");
    writer.println("\tSelectionGroup " + selectionGroup + ",");
    for (int i = 0; i < flags.size(); i++) {
      writer.println("\t" + flags.get(i) + ",");
    }

    writer.println("}");
  }
Esempio n. 12
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  public static Geoset read(BufferedReader mdl) {
    String line = MDLReader.nextLine(mdl);
    System.out.println("geo begins with " + line);
    if (line.contains("Geoset")) {
      line = MDLReader.nextLine(mdl);
      Geoset geo = new Geoset();
      if (!line.contains("Vertices")) {
        JOptionPane.showMessageDialog(
            MDLReader.getDefaultContainer(), "Error: Vertices not found at beginning of Geoset!");
      }
      while (!((line = MDLReader.nextLine(mdl)).contains("\t}"))) {
        geo.addVertex(GeosetVertex.parseText(line));
      }
      line = MDLReader.nextLine(mdl);
      if (line.contains("Normals")) {
        // If we have normals:
        while (!((line = MDLReader.nextLine(mdl)).contains("\t}"))) {
          geo.addNormal(Normal.parseText(line));
        }
      }
      while (((line = MDLReader.nextLine(mdl)).contains("TVertices"))) {
        geo.addUVLayer(UVLayer.read(mdl));
      }
      if (!line.contains("VertexGroup")) {
        JOptionPane.showMessageDialog(
            MDLReader.getDefaultContainer(), "Error: VertexGroups missing or invalid!");
      }
      int i = 0;
      while (!((line = MDLReader.nextLine(mdl)).contains("\t}"))) {
        geo.getVertex(i).setVertexGroup(MDLReader.readInt(line));
        i++;
      }
      line = MDLReader.nextLine(mdl);
      if (!line.contains("Faces")) {
        JOptionPane.showMessageDialog(
            MDLReader.getDefaultContainer(), "Error: Faces missing or invalid!");
      }
      line = MDLReader.nextLine(mdl);
      if (!line.contains("Triangles")) {
        System.out.println(line);
        JOptionPane.showMessageDialog(
            MDLReader.getDefaultContainer(), "Error: Triangles missing or invalid!");
      }
      geo.setTriangles(Triangle.read(mdl, geo));
      line = MDLReader.nextLine(mdl); // Throw away the \t} closer for faces
      line = MDLReader.nextLine(mdl);
      if (!line.contains("Groups")) {
        JOptionPane.showMessageDialog(
            MDLReader.getDefaultContainer(), "Error: Groups (Matrices) missing or invalid!");
      }
      while (!((line = MDLReader.nextLine(mdl)).contains("\t}"))) {
        geo.addMatrix(Matrix.parseText(line));
      }
      MDLReader.mark(mdl);
      line = MDLReader.nextLine(mdl);
      while (!line.contains("}") || line.contains("},")) {
        if (line.contains("Extent") || line.contains("BoundsRadius")) {
          System.out.println("Parsing geoset extLog:" + line);
          MDLReader.reset(mdl);
          geo.setExtLog(ExtLog.read(mdl));
          System.out.println("Completed geoset extLog.");
        } else if (line.contains("Anim")) {
          MDLReader.reset(mdl);
          geo.add(Animation.read(mdl));
          MDLReader.mark(mdl);
        } else if (line.contains("MaterialID")) {
          geo.materialID = MDLReader.readInt(line);
          MDLReader.mark(mdl);
        } else if (line.contains("SelectionGroup")) {
          geo.selectionGroup = MDLReader.readInt(line);
          MDLReader.mark(mdl);
        } else {
          geo.addFlag(MDLReader.readFlag(line));
          System.out.println("Reading to geoFlag: " + line);
          MDLReader.mark(mdl);
        }
        line = MDLReader.nextLine(mdl);
      }
      //             JOptionPane.showMessageDialog(MDLReader.getDefaultContainer(),"Geoset reading
      // completed!");
      System.out.println("Geoset reading completed!");

      return geo;
    } else {
      JOptionPane.showMessageDialog(
          MDLReader.getDefaultContainer(),
          "Unable to parse Geoset: Missing or unrecognized open statement '" + line + "'.");
    }
    return null;
  }
Esempio n. 13
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  private static void addSprites(Compositor sh) throws IOException, QTException {
    File matchFile =
        QTFactory.findAbsolutePath("images/Ship01.pct"); // this file must exist in the directory!!!
    ImageDataSequence isp = ImageUtil.createSequence(matchFile);
    ImageDataSequence seq = ImageUtil.makeTransparent(isp, QDColor.blue);

    // Build Sprites
    Matrix matrix1 = new Matrix();
    matrix1.setTx(20);
    matrix1.setTy(20);
    matrix1.setSx(0.8F);
    matrix1.setSy(0.8F);
    TwoDSprite s1 = new TwoDSprite(seq, 4, matrix1, true, 1);
    sh.addMember(s1);

    Matrix matrix2 = new Matrix();
    matrix2.setTx(4);
    matrix2.setTy(4);
    TwoDSprite s2 = new TwoDSprite(seq, 1, matrix2, true, 10);
    sh.addMember(s2);

    // This needs to be a 32bit QDGraphics so the blend mode will
    // be applied correctly to this sprite
    File shipFile = QTFactory.findAbsolutePath("images/Ship10.pct");
    GraphicsImporterDrawer ip = new GraphicsImporterDrawer(new QTFile(shipFile));
    QDRect r = new QDRect(ip.getDescription().getWidth(), ip.getDescription().getHeight());
    ImageSpec si =
        ImageUtil.makeTransparent(
            ip, QDColor.blue, new QDGraphics(QDGraphics.kDefaultPixelFormat, r));
    Matrix matrix3 = new Matrix();
    matrix3.setTx(50);
    matrix3.setTy(50);
    TwoDSprite s3 =
        new TwoDSprite(si, matrix3, true, 8, new GraphicsMode(QDConstants.blend, QDColor.green));
    sh.addMember(s3);

    // Add Dragger (DEPRECATED CODE)
    /*		Dragger dragger = new Dragger (InputEvent.SHIFT_MASK);
    SWController controller = new SWController (dragger, true);
    sh.addController (controller);*/

    QTMouseTargetController shipController = new QTMouseTargetController(true);
    shipController.addQTMouseListener(
        new DragAction(new TranslateMatrix()) {
          // only activates when the shift modifier is pressed
          public boolean matchModifierFilter(int mods) {
            if ((mods & 0xF) == QTConstants.kJavaShiftMask) return true;
            return false;
          }
        });
    sh.addController(shipController);

    // Add Controllers
    // Build ActionList
    SimpleActionList al = new SimpleActionList();
    ImageSequencer is = new ImageSequencer(seq);
    is.setLooping(ImageSequencer.kLoopForwards);
    al.addMember(new NextImageAction(10, 1, is, s1));
    al.addMember(new BounceAction(5, 1, sh, s1, 3, 2));
    ImageSequencer is2 = new ImageSequencer(seq);
    is2.setLooping(ImageSequencer.kLoopForwards);
    al.addMember(new NextImageAction(20, 1, is2, s2));
    al.addMember(new BounceAction(20, 1, sh, s2, 4, 3));
    sh.addController(al);
  }
Esempio n. 14
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  /**
   * Compute the label's screen position from its geographic position.
   *
   * @param dc Current draw context.
   */
  protected void computeGeometry(DrawContext dc) {
    // Project the label position onto the viewport
    Position pos = this.getPosition();
    if (pos == null) return;

    this.placePoint = dc.computeTerrainPoint(pos.getLatitude(), pos.getLongitude(), 0);
    this.screenPlacePoint = dc.getView().project(this.placePoint);

    this.eyeDistance = this.placePoint.distanceTo3(dc.getView().getEyePoint());

    boolean orientationReversed = false;
    if (this.orientationPosition != null) {
      // Project the orientation point onto the screen
      Vec4 orientationPlacePoint =
          dc.computeTerrainPoint(
              this.orientationPosition.getLatitude(), this.orientationPosition.getLongitude(), 0);
      Vec4 orientationScreenPoint = dc.getView().project(orientationPlacePoint);

      this.rotation = this.computeRotation(this.screenPlacePoint, orientationScreenPoint);

      // The orientation is reversed if the orientation point falls to the right of the screen
      // point. Text is
      // never drawn upside down, so when the orientation is reversed the text flips vertically to
      // keep the text
      // right side up.
      orientationReversed = (orientationScreenPoint.x <= this.screenPlacePoint.x);
    }

    this.computeBoundsIfNeeded(dc);

    Offset offset = this.getOffset();
    Point2D offsetPoint =
        offset.computeOffset(this.bounds.getWidth(), this.bounds.getHeight(), null, null);

    // If a rotation is applied to the text, then rotate the offset as well. An offset in the x
    // direction
    // will move the text along the orientation line, and a offset in the y direction will move the
    // text
    // perpendicular to the orientation line.
    if (this.rotation != null) {
      double dy = offsetPoint.getY();

      // If the orientation is reversed we need to adjust the vertical offset to compensate for the
      // flipped
      // text. For example, if the offset normally aligns the top of the text with the place point
      // then without
      // this adjustment the bottom of the text would align with the place point when the
      // orientation is
      // reversed.
      if (orientationReversed) {
        dy = -(dy + this.bounds.getHeight());
      }

      Vec4 pOffset = new Vec4(offsetPoint.getX(), dy);
      Matrix rot = Matrix.fromRotationZ(this.rotation.multiply(-1));

      pOffset = pOffset.transformBy3(rot);

      offsetPoint = new Point((int) pOffset.getX(), (int) pOffset.getY());
    }

    int x = (int) (this.screenPlacePoint.x + offsetPoint.getX());
    int y = (int) (this.screenPlacePoint.y - offsetPoint.getY());

    this.screenPoint = new Point(x, y);
    this.screenExtent = this.computeTextExtent(x, y, this.rotation);
  }
Esempio n. 15
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  /**
   * Constructor
   *
   * @param f1 FPoint2
   * @param f2 FPoint2
   * @param pt FPoint2, or null for bisector
   */
  private void construct(FPoint2 f1, FPoint2 f2, FPoint2 pt) {

    //    userData[LEFT] = new DArray();
    //    userData[RIGHT]  =new DArray();

    final boolean db = false;
    if (db) {
      System.out.println("Hyperbola constructor\n f1=" + f1 + "\n f2=" + f2 + "\n pt=" + pt);
    }
    boolean bisector = (pt == null);
    initializeVisibleSegments();

    // if point on arm is closer to f2 than f1, swap f1 & f2.

    if (!bisector && FPoint2.distanceSquared(f1, pt) > FPoint2.distanceSquared(f2, pt)) {
      flipped = true;
    }

    this.foci[RIGHT] = new FPoint2(f1);
    this.foci[LEFT] = new FPoint2(f2);
    if (!bisector) {
      this.pt = new FPoint2(pt);
    }

    double fociDist = FPoint2.distance(f1, f2);
    if (fociDist == 0) {
      throw new FPError("Hyperbola foci are same point");
    }

    c = fociDist * .5;

    // calculate the translation of the hyperbola away from
    // standard position.

    FPoint2 rFocus = getFocus(0), lFocus = getFocus(1);

    origin = new FPoint2(.5 * (rFocus.x + lFocus.x), .5 * (rFocus.y + lFocus.y));

    // calculate the angle of rotation of the hyperbola away
    // from the standard position.

    double theta = Math.atan2(rFocus.y - lFocus.y, rFocus.x - lFocus.x);

    Matrix fromCenterInW = Matrix.getTranslate(origin, true);
    Matrix rotToE = Matrix.getRotate(-theta);

    toE2 = rotToE;
    Matrix.mult(toE2, fromCenterInW, toE2);
    // calculate inverse

    toW2 = toE2.invert(null);

    //      Matrix toCenterInW = Matrix.translationMatrix(origin, false);
    //      Matrix rotToW = Matrix.getRotate2D(theta);
    //
    //      toW2 = toCenterInW;
    //      Matrix.mult(toW2, rotToW, toW2);
    //      Tools.warn("just invert matrix here");
    //

    if (bisector) {
      valid = true;
    } else {
      // get the arm point in hyperbola space.
      FPoint2 workPt = toE2.apply(pt, null);

      double xs = workPt.x * workPt.x;
      double cs = c * c;

      Polyn q = new Polyn(1, -(cs + xs + workPt.y * workPt.y), cs * xs);
      if (db) {
        System.out.println("a2 quadratic:\n" + q);
      }
      final DArray qsoln = new DArray();
      q.solve(qsoln);
      if (db) {
        Streams.out.println(qsoln);
      }
      double val = q.c(1) * -.5;
      int ql = qsoln.size();
      if (ql >= 1) {
        val = qsoln.getDouble(0);
      }

      // choose the root that is less than c*c.

      if (ql == 2) {
        if (val > qsoln.getDouble(1)) {
          val = qsoln.getDouble(1);
          if (db) {
            System.out.println(" two roots, choosing smaller.");
          }
        }
      }
      if (db) {
        System.out.println(" root chosen=" + val);
      }

      a = Polyn.sqrt(val);
      A = a * a;
      B = A / (c * c - A);
    }
    valid = true;
    if (db) {
      System.out.println(" ==> " + this);
    }
  }
Esempio n. 16
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  /**
   * ************************************************************* Official Method for setting the
   * zoom and location for heatmap DO NOT IMPLEMENT A NEW FUNCTION Make the necessary
   * customizations, then call this function
   * *************************************************************
   *
   * @param newZoom
   * @param genomeX
   * @param genomeY
   * @param scaleFactor (pass -1 if scaleFactor should be calculated)
   * @return
   */
  public boolean unsafeActuallySetZoomAndLocation(
      String chrXName,
      String chrYName,
      HiCZoom newZoom,
      int genomeX,
      int genomeY,
      double scaleFactor,
      boolean resetZoom,
      ZoomCallType zoomCallType,
      boolean allowLocationBroadcast) {

    if (dataset == null) return false; // No data in view

    // Check this zoom operation is possible, if not, fail it here:
    //        if (superAdapter.testNewZoom(newZoom))
    //        {
    //            return false;
    //        }

    // String chr1OriginalName = xContext.getChromosome().getName();
    // String chr2OriginalName = yContext.getChromosome().getName();
    if (chrXName.length() > 0 && chrYName.length() > 0) {
      setChromosomesFromBroadcast(chrXName, chrYName);
      // We might end with All->All view, make sure normalization state is updates accordingly...
      superAdapter.getMainViewPanel().setNormalizationDisplayState(superAdapter.getHiC());
    }

    if (newZoom == null) {
      System.err.println("Invalid zoom " + newZoom);
    }

    Chromosome chr1 = xContext.getChromosome();
    Chromosome chr2 = yContext.getChromosome();
    final Matrix matrix = dataset.getMatrix(chr1, chr2);

    if (matrix == null) {
      superAdapter.launchGenericMessageDialog(
          "Sorry, this region is not available", "Matrix unavailable", JOptionPane.WARNING_MESSAGE);
      return false;
    }

    MatrixZoomData newZD = matrix.getZoomData(newZoom);
    if (HiCFileTools.isAllChromosome(chr1)) {
      newZD = matrix.getFirstZoomData(Unit.BP);
    }

    if (newZD == null) {
      superAdapter.launchGenericMessageDialog(
          "Sorry, this zoom is not available", "Zoom unavailable", JOptionPane.WARNING_MESSAGE);
      return false;
    }

    /* TODO Undo Zoom implementation mss2 _UZI
    if(currentZoom != null) {
        tempZoomState = new ZoomState(chr1OriginalName, chr2OriginalName, currentZoom.clone(), (int) xContext.getBinOrigin(),
                (int) yContext.getBinOrigin(), getScaleFactor(), resetZoom, ZoomCallType.GOTO);
    }
    */

    currentZoom = newZoom;
    xContext.setZoom(currentZoom);
    yContext.setZoom(currentZoom);

    if (scaleFactor > 0) {
      setScaleFactor(scaleFactor);
    } else {
      int maxBinCount =
          Math.max(newZD.getXGridAxis().getBinCount(), newZD.getYGridAxis().getBinCount());
      double defaultScaleFactor =
          Math.max(
              1.0, (double) superAdapter.getHeatmapPanel().getMinimumDimension() / maxBinCount);
      setScaleFactor(defaultScaleFactor);
    }

    int binX = newZD.getXGridAxis().getBinNumberForGenomicPosition(genomeX);
    int binY = newZD.getYGridAxis().getBinNumberForGenomicPosition(genomeY);
    switch (zoomCallType) {
      case INITIAL:
      case STANDARD:
        center(binX, binY);
        break;
      case DRAG:
        xContext.setBinOrigin(binX);
        yContext.setBinOrigin(binY);
        break;
      case DIRECT:
        xContext.setBinOrigin(genomeX);
        yContext.setBinOrigin(genomeY);
        break;
    }

    // Notify HeatmapPanel render that zoom has changed. Render should update zoom slider once with
    // previous range values

    setZoomChanged();
    if (resetZoom) {
      superAdapter.updateAndResetZoom(newZoom);
    } else {
      superAdapter.updateZoom(newZoom);
    }
    superAdapter.refresh();

    if (linkedMode && allowLocationBroadcast) {
      broadcastLocation();
    }
    /*
    TODO Undo Zoom implementation mss2 _UZI
    if(zoomCallType == ZoomCallType.INITIAL || tempZoomState == null || chrXName.equals(Globals.CHR_ALL) || chrYName.equals(Globals.CHR_ALL)
            || tempZoomState.chr1Name.equals(Globals.CHR_ALL) || tempZoomState.chr2Name.equals(Globals.CHR_ALL)){
        canRedoZoomChange = false;
        canUndoZoomChange = false;
    }
    else {
        // defauts for a normal zoom operation
        canRedoZoomChange = false;
        canUndoZoomChange = true;
        previousZoomState = tempZoomState;
    }
    */

    return true;
  }