/**
* The inner array is an array of 2 colors, for alternating exon colors. The "outer" array
* represents transcript coloring. Transcripts can have different exon coloring pairs(see
* SelectableDNARenderer's exonColorIndex and transcriptColorIndex). This now takes in 2 colors
* from Config edeFeatureColor. It no longer is setting up 4 colors for alternating transcripts as
* well as exons. Easy enough to reinstate if desired.
*/
public Color[][] getColorArray() {
Color firstExonColor = Config.getExonDetailEditorFeatureColor1();
Color secondExonColor = Config.getExonDetailEditorFeatureColor2();
Color[][] colors = {{firstExonColor, secondExonColor}};
// Color [][] colors = {{Color.blue, new Color(0,0,180)},
// {new Color(100,150,255), new Color(100,0,200)}};
return colors;
}
public String generateURL(SeqFeatureI f) {
if (f instanceof AnnotatedFeatureI)
// For now, all annotations share a common base URL, defined in the style
// file as ExternalRefURL.
return generateAnnotURL((AnnotatedFeatureI) f, Config.getExternalRefURL());
else return generateAnalysisURL(f);
}
private String generateAnalysisURL(SeqFeatureI f) {
// Figure out URL for getting more information about this feature.
// If more than one feature was selected, use the LAST one.
String id = getIdForURL(f);
FeatureProperty prop = Config.getPropertyScheme().getFeatureProperty(f.getFeatureType());
String urlPrefix = getURLPrefix(prop, f, id);
if (urlPrefix == null) {
String m =
"Sorry, no URL registered for type "
+ f.getFeatureType()
+ "\nin tiers file "
+ Config.getStyle().getTiersFile();
JOptionPane.showMessageDialog(null, m);
return null;
}
return URLQueryGenerator.getURL(urlPrefix, id);
}
public void setGene(AnnotatedFeatureI g) {
this.gene = g;
if (g == null) return;
if (!g.isProteinCodingGene()) {
setText("NOT A PEPTIDE");
setEnabled(false);
} else {
setEnabled(true);
Hashtable curator_values = Config.getPeptideStates();
String pep_status = g.getProperty("sp_status");
PeptideStatus this_status = Config.getPeptideStatus(pep_status);
JMenuItem item;
/* these are the computed values that cannot be over-ridden
by a curator
*/
item = new JMenuItem(this_status.getText());
add(item);
item.addActionListener(this);
/* these are the possible values to be selected
by a curator */
Enumeration e = curator_values.keys();
while (e.hasMoreElements()) {
String key = (String) e.nextElement();
PeptideStatus a_status = (PeptideStatus) curator_values.get(key);
if (a_status.getPrecedence() >= this_status.getPrecedence()
&& !a_status.getText().equals(this_status.getText())
&& a_status.getCurated()) {
item = new JMenuItem(a_status.getText());
add(item);
item.addActionListener(this);
}
}
setText(this_status.getText());
}
}
public TypesMenu(AnnotationEditor editor) {
super("Create new annotation");
this.editor = editor;
// setEnabled(false);
PropertyScheme scheme = Config.getPropertyScheme();
Vector annotFeatureProps = scheme.getAnnotationFeatureProps();
Iterator props = annotFeatureProps.iterator();
while (props.hasNext()) {
String type = ((FeatureProperty) props.next()).getDisplayType();
JMenuItem typeItem = new JMenuItem(type);
add(typeItem);
typeItem.addActionListener(this);
typeItem.setBackground(scheme.getFeatureProperty(type).getColour());
}
}
/* Note: low and high are relative coordinates */
protected String getResiduesFromSourceImpl(int low, int high) {
int realStart = low; // + getRange().getStart();
int realEnd = high; // + getRange().getStart();
Hashtable var = new Hashtable();
// var.put("bp_start",String.valueOf(new Integer(realStart)));
// var.put("bp_end", String.valueOf(new Integer(realEnd)));
// var.put("chr",getRange().getName());
// var.put("type","basepairs");
// var.put("format","fasta");
// var.put("region","1");
// var.put("btnsubmit","Export");
// var.put("tab","fasta");
// http://dev.ensembl.org:80/perl/exportview?tab=fasta&btnsubmit=Export&format=fasta®ion=1&type=basepairs&chr=2&bp_start=123&bp_end=100000
var.put("vc_start", String.valueOf(new Integer(realStart)));
var.put("vc_end", String.valueOf(new Integer(realEnd)));
var.put("chr", getRange().getName());
var.put("seqonly", "1");
// http://dev.ensembl.org:80/perl/exportview?tab=fasta&btnsubmit=Export&format=fasta®ion=1&type=basepairs&chr=2&bp_start=123&bp_end=100000
String host = server;
int port = Config.getCGIPort();
String cgistr = "perl/apolloview";
// String cgistr = "perl/exportview";
CGI cgi = new CGI(host, port, cgistr, var, System.out);
cgi.run();
FastaFile fa = new FastaFile(cgi.getInput(), false);
Vector seqs = fa.getSeqs();
if (seqs.size() == 1) {
System.out.println("Returning sequence");
return ((SequenceI) seqs.elementAt(0)).getResidues();
} else {
System.out.println("Returning null");
return null;
}
}
/** For annotations, try to find the appropriate identifier to add to the base URL. */
protected String generateAnnotURL(AnnotatedFeatureI g, String baseAnnotURL) {
if (baseAnnotURL == null || baseAnnotURL.equals("")) return null;
Hashtable id_hash = new Hashtable();
String id;
for (int i = 0; i < g.getDbXrefs().size(); i++) {
DbXref ref = (DbXref) g.getDbXrefs().elementAt(i);
id = ref.getIdValue();
// Apparently, if the id starts with FBan we want to replace "FBan" with "CG".
if (id.startsWith("FBan")) {
id = id.substring("FBan".length());
try {
int cg_num = Integer.parseInt(id);
id = "CG" + cg_num;
id_hash.put(id, id);
} catch (Exception e) {
}
} else if (id.startsWith("FB")) { // FBgn, FBab, etc.
id_hash.put(id, id);
} else if (id.startsWith("TE")) { // FBgn, FBab, etc.
id_hash.put(id, id);
}
}
id = getCG(g.getId(), "CG");
if (id != null) id_hash.put(id, id);
else {
id = getCG(g.getId(), "CR");
if (id != null) id_hash.put(id, id);
else {
id = getCG(g.getId(), "FB");
if (id != null) id_hash.put(id, id);
}
}
id = getCG(g.getName(), "CG");
if (id != null) id_hash.put(id, id);
else {
id = getCG(g.getName(), "CR");
if (id != null) id_hash.put(id, id);
}
for (int i = 0; i < g.getSynonyms().size(); i++) {
Synonym syn = (Synonym) (g.getSynonyms().elementAt(i));
id = getCG(syn.getName(), "CG");
if (id != null) id_hash.put(id, id);
else {
id = getCG(syn.getName(), "CR");
if (id != null) id_hash.put(id, id);
else {
id = getCG(g.getId(), "FB");
if (id != null) id_hash.put(id, id);
}
}
}
// The code here was glomming together all the elements into one
// big |ed string, but that's not what the FlyBase annotation report CGI wants.
// An FB or CG or CR identifier should be sufficient.
StringBuffer query_str = new StringBuffer();
for (Enumeration e = id_hash.elements(); e.hasMoreElements(); ) {
String namepart = (String) e.nextElement();
// System.out.println("Considering namepart " + namepart); // DEL
if (namepart.indexOf("FB") == 0
|| namepart.indexOf("CG") == 0
|| namepart.indexOf("CR") == 0) {
if (query_str.length() > 0) query_str.replace(0, query_str.length(), namepart);
else query_str.append(namepart);
break;
}
if (query_str.length() > 0) query_str.append('|');
query_str.append(namepart);
}
// if not FlyBase ID, use the annotation's regular ID
if (query_str.length() == 0) {
query_str.append(g.getId());
}
String url = null;
// System.out.println("generateAnnotUrl: query = " + query_str); // DEL
if (query_str.length() > 0) {
// if a custom URL is setup for this type in the tiers file, use that - otherwise use the
// global
// one setup in the style file
FeatureProperty fp = Config.getPropertyScheme().getFeatureProperty(g.getTopLevelType());
if (fp.getURLString() != null && fp.getURLString().length() > 0) {
url = fp.getURLString() + g.getId();
} else {
url = baseAnnotURL + query_str.toString();
}
}
return url;
}
public class AminoAcidRenderer extends DefaultBaseRenderer {
private static Hashtable colors = new Hashtable();
Color bgcolor;
Color disabled = new Color(200, 200, 200);
int phase;
Font regularFont = apollo.config.Config.getExonDetailEditorSequenceFont();
Font boldFont = apollo.config.Config.getExonDetailEditorSequenceFont();
SeqAlignPanel panel;
Color hatchColor;
static {
colors.put("M", Color.green);
colors.put("*", Color.red);
}
public AminoAcidRenderer(int width, int height, int phase, SeqAlignPanel panel) {
super(width, height);
setFontSizes(12);
this.phase = phase;
this.panel = panel;
}
public void setFontSizes(int size) {
regularFont = new Font("Courier", 0, size);
boldFont = new Font("Dialog", Font.BOLD, size);
}
public Color getHatchColor() {
return hatchColor;
}
public Component getBaseRendererComponent(char base, int pos, int tier, SequenceI seq) {
if (panel instanceof BaseEditorPanel && ((BaseEditorPanel) panel).getShowHitZones()) {
Vector hitZones = ((BaseEditorPanel) panel).getTranslatedHitZones(phase);
hatchColor = null;
for (int hitIndex = 0; hitZones != null && hitIndex < hitZones.size(); hitIndex++) {
int[] hitZone = (int[]) hitZones.elementAt(hitIndex);
if (pos >= hitZone[0] * 3 + phase && pos < hitZone[1] * 3 + phase) {
hatchColor = Color.yellow;
break;
}
}
}
if (colors.get(base + "") == null) setFont(regularFont);
else setFont(boldFont);
return super.getBaseRendererComponent(base, pos, tier, seq);
}
public Color getTextColor() {
Color stored = (Color) colors.get(c + "");
if (stored == null) return disabled;
else return stored;
}
}
public boolean keep(SeqFeatureI f) {
FeatureProperty fp = Config.getPropertyScheme().getFeatureProperty(f.getTopLevelType());
return displayType.equalsIgnoreCase(fp.getDisplayType());
}
public class SelectableDNARenderer extends DefaultBaseRenderer {
protected final Color[][] transcriptColorList;
protected int transcriptColorIndex = 0;
protected int exonColorIndex = 0;
SeqAlignPanel baseEditor;
double currentRange[] = new double[2];
double transcriptRange[] = new double[2];
double oldRange[] = new double[2];
SeqFeatureI currentFeature;
FeatureSetI currentFeatureSet;
int type;
boolean isIntron;
boolean isExon;
int targetNucleotide = -1;
int targetTier = -1;
int hitIndex;
Color targetColor;
Color seqSelectColor;
Color hatchColor;
// Color shiftColor = new Color(255, 153, 0); // bright orange
Color shiftColor = apollo.config.Config.getStyle().getSeqErrorColor();
public SelectableDNARenderer(SeqAlignPanel baseEditor, int width, int height) {
super(width, height);
this.baseEditor = baseEditor;
if (baseEditor instanceof BaseEditorPanel) {
transcriptColorList = ((BaseEditorPanel) baseEditor).getColorArray();
setSeqSelectColor(((BaseEditorPanel) baseEditor).getSeqSelectColor());
} else {
transcriptColorList = new Color[1][1];
transcriptColorList[0][0] = Color.blue;
setSeqSelectColor(Color.pink);
}
// setTargetColor(Color.yellow);
setTargetColor(shiftColor);
}
public void setTargetPos(int pos, int tier) {
targetNucleotide = pos;
targetTier = tier;
}
public void setTargetColor(Color in) {
targetColor = in;
}
public void setSeqSelectColor(Color in) {
seqSelectColor = in;
}
public void paintNotify() {
currentRange[0] = Double.POSITIVE_INFINITY;
currentRange[1] = Double.NEGATIVE_INFINITY;
transcriptRange[0] = Double.POSITIVE_INFINITY;
transcriptRange[1] = Double.NEGATIVE_INFINITY;
currentFeature = null;
transcriptColorIndex = 0;
exonColorIndex = 0;
hitIndex = 0;
}
/**
* Get component to be rendered, if pos outside of current range getFeatureAtPosition and reset
* currentRange, if feature is non null and not an instance of FeatureSetI then its an exon, and
* set isExon flag
*/
public Component getBaseRendererComponent(char base, int pos, int tier, SequenceI seq) {
init(base, pos, tier, seq);
hatchColor = null;
if (((BaseEditorPanel) baseEditor).getShowHitZones()) {
Vector hitZones = ((BaseEditorPanel) baseEditor).hitZones;
for (int hitIndex = 0; hitIndex < hitZones.size(); hitIndex++) {
int[] hitZone = (int[]) hitZones.elementAt(hitIndex);
if (pos >= hitZone[0] && pos < hitZone[1]) {
hatchColor = Color.yellow;
break;
}
}
}
currentFeature = baseEditor.getFeatureAtPosition(pos, tier);
double[] range = establishRange(currentFeature, pos, tier, false);
if (range[1] != currentRange[1] || range[0] != currentRange[0]) {
currentRange[0] = range[0];
currentRange[1] = range[1];
currentFeatureSet = baseEditor.getFeatureSetAtPosition(pos, tier);
range = establishRange(currentFeatureSet, pos, tier, true);
transcriptRange[0] = range[0];
transcriptRange[1] = range[1];
if (currentFeature != null) {
// This decides the index into the color array, transcripts
// can have different colors for their features
transcriptColorIndex =
(baseEditor.getRangeIndex(tier, (int) currentRange[0], (int) currentRange[1]))
% transcriptColorList.length;
exonColorIndex =
(baseEditor.getExonRangeIndex(tier, (int) currentRange[0], (int) currentRange[1]))
% transcriptColorList[transcriptColorIndex].length;
}
if (currentFeature == null) {
isExon = false;
isIntron = false;
// } else if (currentFeature.canHaveChildren()) {
} else if (currentFeature.hasKids()) { // 1 level annots can but dont
isExon = false;
isIntron = true;
} else {
isExon = true;
isIntron = false;
}
}
return this;
}
/* Establish the currentRange of bases covered by the
currentFeature of this renderer
*/
public double[] establishRange(SeqFeatureI sf, int pos, int tier, boolean use_set) {
double range[];
if (sf == null || (!use_set && (sf.canHaveChildren()))) {
range = baseEditor.getRangeAtPosition(tier, pos);
} else {
range = new double[2];
range[0] = (double) baseEditor.basePairToPos(sf.getLow());
range[1] = (double) baseEditor.basePairToPos(sf.getHigh());
}
return range;
}
public Color getHatchColor() {
return hatchColor;
}
public Color getBackgroundBoxColor() {
if (pos == targetNucleotide && tier == targetTier) return targetColor;
int lowSeqSelect;
int highSeqSelect;
if (baseEditor instanceof BaseEditorPanel) {
lowSeqSelect = ((BaseEditorPanel) baseEditor).selectLowPos();
highSeqSelect = ((BaseEditorPanel) baseEditor).selectHighPos();
} else {
lowSeqSelect = -1;
highSeqSelect = -1;
}
if (lowSeqSelect != -1 && highSeqSelect != -1 && pos >= lowSeqSelect && pos <= highSeqSelect) {
return seqSelectColor;
}
int basePos = baseEditor.posToBasePair(pos);
if (((BaseEditorPanel) baseEditor).isSequencingErrorPosition(basePos)) return shiftColor;
if (isExon) {
ExonI exon = null;
if (currentFeature instanceof ExonI) exon = (ExonI) currentFeature;
else if (currentFeature instanceof DrawableSeqFeature)
exon = (ExonI) ((DrawableSeqFeature) currentFeature).getFeature();
if (exon != null && exon.getTranscript() != null) {
Transcript transcript = exon.getTranscript();
int tss = (int) exon.getTranscript().getTranslationStart();
if (basePos == tss
|| basePos == (tss + exon.getStrand())
|| basePos == (tss + (2 * exon.getStrand())))
return DrawableUtil.getStartCodonColor(transcript);
else {
int tes = (int) transcript.getTranslationEnd();
if (basePos == tes
|| basePos == (tes + exon.getStrand())
|| basePos == (tes + (2 * exon.getStrand()))) return Color.red;
else {
int shift_pos = (int) transcript.plus1FrameShiftPosition();
if (basePos == shift_pos) return shiftColor;
else {
shift_pos = (int) transcript.minus1FrameShiftPosition();
if (basePos == shift_pos) return shiftColor;
else {
int stop_pos = (int) transcript.readThroughStopPosition();
if (basePos == stop_pos
|| basePos == (stop_pos + exon.getStrand())
|| basePos == (stop_pos + (2 * exon.getStrand()))) return Color.pink;
}
}
}
}
}
return transcriptColorList[transcriptColorIndex][exonColorIndex];
}
return null;
}
public Color getBackgroundLineColor() {
if (pos == targetNucleotide && tier == targetTier) return null;
if (isIntron) return transcriptColorList[transcriptColorIndex][0];
return null;
}
public Color getTextColor() {
return Color.white;
}
public void paint(Graphics g) {
g.setFont(getFont());
Color boxColor = getBackgroundBoxColor();
Color hatchColor = getHatchColor();
Color backgroundLineColor = getBackgroundLineColor();
// Color textColor = getForeground();
int outlineType = getOutlineType();
Color outlineColor = getOutlineColor();
if (backgroundLineColor != null) {
g.setColor(backgroundLineColor);
g.fillRect(0, getSize().height / 2 - 1, getSize().width, 2);
}
if (boxColor != null) {
g.setColor(boxColor);
g.fillRect(0, 0, getSize().width, getSize().height);
}
if (hatchColor != null) {
g.setColor(hatchColor);
// Bev thinks the cross-hatching makes it too hard to read the base.
// For a single diagonal line, replace the following three lines with
// g.drawLine(0,getSize().height, getSize().width,0);
// For an underline, replace with
// g.drawLine(0,getSize().height, getSize().width,getSize().height);
// Draw three cross-hatch lines
// g.drawLine(0,0,getSize().width,getSize().height);
// g.drawLine(getSize().width/2,0,getSize().width,getSize().height/2);
// g.drawLine(0,getSize().height/2,getSize().width/2,getSize().height);
// Draw a line at top and bottom of matching base
g.drawLine(0, getSize().height, getSize().width, getSize().height); // bottom
g.drawLine(0, 0, getSize().width, 0); // top
// g.drawLine(0,0, 0,getSize().height); // left side
// g.drawLine(getSize().width,0, getSize().width,getSize().height); // right side
}
if (outlineType != NO_OUTLINE && outlineColor != null) {
g.setColor(outlineColor);
g.drawLine(0, 0, getSize().width - 1, 0);
g.drawLine(0, getSize().height - 1, getSize().width - 1, getSize().height - 1);
if (outlineType == LEFT_OUTLINE) g.drawLine(0, 0, 0, getSize().height - 1);
else if (outlineType == RIGHT_OUTLINE) {
g.drawLine(getSize().width - 1, 0, getSize().width - 1, getSize().height - 1);
}
}
if (getTextColor() != null) {
int leadDistance = (getSize().width - metrics.charWidth(c)) / 2;
g.setColor(getTextColor());
g.drawString(c + "", leadDistance, getSize().height - 2);
}
}
/**
* Checks if selected or selected refs feature is the current feature set, so an exon as well as a
* transcript will have an outline type
*/
public int getOutlineType() {
SeqFeatureI selected = null;
if (baseEditor instanceof BaseEditorPanel) {
selected = ((BaseEditorPanel) baseEditor).getSelectedFeature();
}
if (featSetContainsFeat(currentFeatureSet, selected)) {
if (pos == transcriptRange[0]) return LEFT_OUTLINE;
else if (pos == transcriptRange[1]) return RIGHT_OUTLINE;
else return CENTER_OUTLINE;
}
return NO_OUTLINE;
}
/**
* Checks if selected or selected refs feature is the feature set at current pos, so an exon as
* well as a transcript will have an outline color
*/
public Color getOutlineColor() {
SeqFeatureI selected = null;
if (baseEditor instanceof BaseEditorPanel) {
selected = ((BaseEditorPanel) baseEditor).getSelectedFeature();
}
FeatureSetI featureSet = baseEditor.getFeatureSetAtPosition(pos, tier);
if (featSetContainsFeat(featureSet, selected)) return Color.magenta;
else return null;
}
/** True if feat or feats refFeat is fs */
private boolean featSetContainsFeat(FeatureSetI fs, SeqFeatureI feat) {
if (fs == null || feat == null) return false;
if (fs == feat) return true;
if (fs == feat.getRefFeature()) return true;
// This should probably be generalized(recursive) for whole ancestor tree and added to
// FeatureSetI - for now only need to do feat and ref feat
// could use FeatureSet.find i guess - is that what thats intended for?
return false;
}
public void setTier(int tier) {
this.tier = tier;
}
public boolean canRender(SeqFeatureI feature) {
return feature.isAnnot();
}
}