public void getISUnknownFixedIns() {
Record pair1 = null;
int pair1Index = -1;
Record pair2 = null;
int pair2Index = -1;
for (int i = 0; i < records.size(); i++) {
Record cur = records.get(i);
if (cur.regular) {
if (cur.edgeName1.equals("EDGE:111:239")
&& cur.edgeName2.equals("EDGE:72:203")
&& !cur.fwd1
&& cur.fwd2
&& cur.doesFirstOverlapWith(847025, 847475)
&& cur.doesSecondOverlapWith(1820800, 1821075)) { // pair1
pair1 = cur;
pair1Index = i;
records.remove(i);
i--;
} else if (cur.edgeName1.equals("EDGE:111:239")
&& cur.edgeName2.equals("EDGE:72:203")
&& cur.fwd1
&& !cur.fwd2
&& cur.doesFirstOverlapWith(847700, 848050)
&& cur.doesSecondOverlapWith(1821225, 1821625)) { // pair1
pair2 = cur;
pair2Index = i;
records.remove(i);
i--;
}
}
}
if (pair1Index > -1 && pair2Index > -1) {
System.out.println("*FIXED\n" + pair1 + "\n" + pair2 + "\n");
// records.remove(pair1Index);
// records.remove(pair2Index);
} else if (pair1Index == -1 && pair2Index > -1) {
System.out.println("*FIXED\n**MISSING**\n" + pair2 + "\n");
// records.remove(pair2Index);
} else if (pair1Index > -1 && pair2Index == -1) {
System.out.println("*FIXED\n" + pair1 + "\n**MISSING**\n");
// records.remove(pair1Index);
} else {
System.out.println("*FIXED\n**MISSING**\n**MISSING**\n");
}
}
public void getISDra3FixedIns() {
Record pair1 = null;
int pair1Index = -1;
Record pair2 = null;
int pair2Index = -1;
for (int i = 0; i < records.size(); i++) {
Record cur = records.get(i);
if (cur.regular) {
if (cur.edgeName1.equals("EDGE:137:142")
&& cur.edgeName2.equals("EDGE:184:240")
&& !cur.fwd1
&& !cur.fwd2
&& cur.doesFirstOverlapWith(253050, 253350)
&& cur.doesSecondOverlapWith(1748200, 1748500)) { // pair1
pair1 = cur;
pair1Index = i;
records.remove(i);
i--;
} else if (cur.edgeName1.equals("EDGE:137:142")
&& cur.edgeName2.equals("EDGE:184:240")
&& cur.fwd1
&& cur.fwd2
&& cur.doesFirstOverlapWith(253650, 253950)
&& cur.doesSecondOverlapWith(1747700, 1747950)) { // pair1
pair2 = cur;
pair2Index = i;
records.remove(i);
i--;
}
}
}
if (pair1Index > -1 && pair2Index > -1) {
System.out.println("*FIXED\n" + pair1 + "\n" + pair2 + "\n");
// records.remove(pair1Index);
// records.remove(pair2Index);
} else if (pair1Index == -1 && pair2Index > -1) {
System.out.println("*FIXED\n**MISSING**\n" + pair2 + "\n");
// records.remove(pair2Index);
} else if (pair1Index > -1 && pair2Index == -1) {
System.out.println("*FIXED\n" + pair1 + "\n**MISSING**\n");
// records.remove(pair1Index);
} else {
System.out.println("*FIXED\n**MISSING**\n**MISSING**\n");
}
}
public void removeWrapAround() {
for (int i = 0; i < records.size(); i++) {
Record cur = records.get(i);
if (cur.regular) {
if (cur.edgeName1.equals("EDGE:0:182")
&& cur.edgeName2.equals("EDGE:26:267")
&& !cur.fwd1
&& cur.fwd2
&& cur.doesFirstOverlapWith(100, 400)
&& cur.doesSecondOverlapWith(2648250, 2648550)) { // chromosome 1
System.out.println("WRAP-AROUND FOR chromosome 1:" + records.get(i).recordLine);
records.remove(i);
i--;
} else if (cur.edgeName1.equals("EDGE:26:267")
&& cur.edgeName2.equals("EDGE:129:290")
&& !cur.fwd1
&& cur.fwd2
&& cur.doesFirstOverlapWith(2648750, 2649050)
&& cur.doesSecondOverlapWith(3060550, 3060900)) { // chromosome 2
System.out.println("WRAP-AROUND FOR chromosome 2:" + records.get(i).recordLine);
records.remove(i);
i--;
} else if (cur.edgeName1.equals("EDGE:129:290")
&& cur.edgeName2.equals("EDGE:138:140")
&& !cur.fwd1
&& cur.fwd2
&& cur.doesFirstOverlapWith(3061100, 3061400)
&& cur.doesSecondOverlapWith(3238050, 3238350)) { // MP1
System.out.println("WRAP-AROUND FOR PLASMID MP1:" + records.get(i).recordLine);
records.remove(i);
i--;
} else if (cur.edgeName1.equals("EDGE:138:140")
&& cur.edgeName2.equals("EDGE:29:86")
&& !cur.fwd1
&& cur.fwd2
&& cur.doesFirstOverlapWith(3238600, 3238900)
&& cur.doesSecondOverlapWith(3283500, 3283850)) { // CP1
System.out.println("WRAP-AROUND FOR PLASMID CP1:" + records.get(i).recordLine);
records.remove(i);
i--;
}
}
}
System.out.println("\n");
}