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[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/gui Config.java,1.103,1.104 SyntenyLinkPanel.java,1.11,1.12 SyntenyPanel.java,1.4,1.5
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From: Michele C. <mc...@us...> - 2003-02-27 17:45:03
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Update of /cvsroot/gmod/apollo/src/java/apollo/gui
In directory sc8-pr-cvs1:/tmp/cvs-serv30429/apollo/gui
Modified Files:
Config.java SyntenyLinkPanel.java SyntenyPanel.java
Log Message:
Format in FeatureSetBuilder,Config
SyntenyPanel main method conforms to SyntenyLinkPanel constructor
SyntenyLinkPanel - fixed clustering bug found after many moons.
BlixemRunner - debug to find out why not working. Not found yet.
Index: Config.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/gui/Config.java,v
retrieving revision 1.103
retrieving revision 1.104
diff -C2 -d -r1.103 -r1.104
*** Config.java 25 Feb 2003 23:13:51 -0000 1.103
--- Config.java 27 Feb 2003 17:44:57 -0000 1.104
***************
*** 1073,1077 ****
String osname = System.getProperty("os.name");
// Any other cases?? What about Alphas?
! if (osname.startsWith("Linux") || osname.startsWith("Solaris") || osname.startsWith("Sun") ||
osname.indexOf("ix") > 0)
return true;
--- 1073,1077 ----
String osname = System.getProperty("os.name");
// Any other cases?? What about Alphas?
! if (osname.startsWith("Linux") || osname.startsWith("Solaris") || osname.startsWith("Sun") || osname.startsWith("Mac OS X") ||
osname.indexOf("ix") > 0)
return true;
Index: SyntenyLinkPanel.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/gui/SyntenyLinkPanel.java,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** SyntenyLinkPanel.java 27 Feb 2003 14:52:06 -0000 1.11
--- SyntenyLinkPanel.java 27 Feb 2003 17:44:57 -0000 1.12
***************
*** 465,469 ****
}
-
QuickSort.sort(featStart,feat);
QuickSort.sort(featHStart,hfeat);
--- 465,468 ----
***************
*** 480,486 ****
int reverseCount = 0;
- //System.out.println("Max dist " + maxDist);
- //System.out.println("Max size " + minSize);
-
Vector featHolder = new Vector();
--- 479,482 ----
***************
*** 492,523 ****
double dist2 = (1.0*Math.abs(feat[i].getHLow() - prev.getHLow()));
- //int internum = find_internum(feat[i],prev,feat);
-
int internum = 0;
- //int internum = find_internum(feat[i],prev,hfeat);
! //System.out.println("Dist is " + dist1 + " " + dist2 + " " + internum);
// We've reached the end of a block
if ((dist1 > maxDist) || (dist2 > maxDist) || internum > 5) {
double size1 = Math.abs(maxStart - minStart);
double size2 = Math.abs(maxHStart - minHStart);
- //System.out.println("Distance too big");
-
- //System.out.println("Sizes " + size1 + " " + size2 + " " + internum);
// Is the block big enough to keep?
if (size1 > minSize && size2 > minSize) {
- //System.out.println("Size is big enough to keep " + size1 + " " + size2);
-
- //SeqFeature sf1 = new SeqFeature(feat[i].getName(), minStart, maxStart, "synten");
- //SeqFeature sf2 = new SeqFeature(feat[i].getHname(),minHStart,maxHStart,"synten");
SeqFeature sf1 = new SeqFeature(minStart,maxStart,prev.getType());
- sf1.setName(prev.getName());
-
SeqFeature sf2 = new SeqFeature(minHStart,maxHStart,prev.getType());
sf2.setName(prev.getHname());
--- 488,509 ----
double dist2 = (1.0*Math.abs(feat[i].getHLow() - prev.getHLow()));
int internum = 0;
! System.out.println("Dist is " + feat[i].getHname() + " " + dist1 + " " + dist2 + " " + internum);
// We've reached the end of a block
if ((dist1 > maxDist) || (dist2 > maxDist) || internum > 5) {
+
double size1 = Math.abs(maxStart - minStart);
double size2 = Math.abs(maxHStart - minHStart);
// Is the block big enough to keep?
if (size1 > minSize && size2 > minSize) {
SeqFeature sf1 = new SeqFeature(minStart,maxStart,prev.getType());
SeqFeature sf2 = new SeqFeature(minHStart,maxHStart,prev.getType());
+ sf1.setName(prev.getName());
sf2.setName(prev.getHname());
***************
*** 536,552 ****
}
-
-
-
FeaturePair fp = new FeaturePair(sf1,sf2);
- //System.out.println("Feature is " + fp.getLow() + " " + fp.getHigh() + " " + fp.getHLow() + " " + fp.getHHigh());
-
newfset.addFeature(fp);
linkHash.put(fp,featHolder);
- } else {
- // System.out.println("Size too small");
}
!
prev = null;
--- 522,531 ----
}
FeaturePair fp = new FeaturePair(sf1,sf2);
newfset.addFeature(fp);
linkHash.put(fp,featHolder);
}
!
prev = null;
***************
*** 560,568 ****
featHolder = new Vector();
}
}
-
if (feat[i].getLow() < minStart) {
minStart = feat[i].getLow();
--- 539,548 ----
featHolder = new Vector();
+
+ System.out.println("Starting new block " + feat[i].getName());
}
}
if (feat[i].getLow() < minStart) {
minStart = feat[i].getLow();
***************
*** 581,585 ****
}
! //System.out.println("New region bounds " + minStart + " " + maxStart + " " + minHStart + " " + maxHStart);
if (prev != null) {
--- 561,565 ----
}
! System.out.println("New region bounds " + minStart + " " + maxStart + " " + minHStart + " " + maxHStart);
if (prev != null) {
***************
*** 651,655 ****
for (int i=0; i < newfset.size(); i++) {
FeaturePair fp = (FeaturePair)newfset.getFeatureAt(i);
! System.out.println("Processing feature " + fp.getLow() + " " + fp.getHigh() + " - " + fp.getHLow() + " " + fp.getHHigh());
if (prev != null) {
--- 631,635 ----
for (int i=0; i < newfset.size(); i++) {
FeaturePair fp = (FeaturePair)newfset.getFeatureAt(i);
! System.out.println("Processing feature " + fp.getHname() + " " + fp.getLow() + " " + fp.getHigh() + " - " + fp.getHLow() + " " + fp.getHHigh());
if (prev != null) {
***************
*** 660,674 ****
double dist1 = Math.abs(fp.getLow() - prev.getHigh());
double dist2 = Math.abs(fp.getHLow() - prev.getHHigh());
if (fp.getHstrand() == -1) {
dist2 = Math.abs(fp.getHHigh() - prev.getHLow());
}
- System.out.println("Distances " + dist1 + " " + dist2 + " " + (Math.abs(dist1 - dist2)));
System.out.println("Pog " + internum + " " + ori);
! if ((Math.abs(dist1 - dist2) > (maxDist * 10)) || internum > 0 || ori == -1) {
! System.out.println("New block " + Math.abs(dist1 - dist2));
SeqFeature sf1 = new SeqFeature(minStart ,maxStart ,"synten");
--- 640,655 ----
double dist1 = Math.abs(fp.getLow() - prev.getHigh());
double dist2 = Math.abs(fp.getHLow() - prev.getHHigh());
+
if (fp.getHstrand() == -1) {
dist2 = Math.abs(fp.getHHigh() - prev.getHLow());
}
+ System.out.println("Distances " + dist1 + " " + dist2 + " " + (Math.abs(dist1 - dist2)));
System.out.println("Pog " + internum + " " + ori);
! if ((Math.abs(dist1 - dist2) > (maxDist * 10)) || internum > 0 || ori == -1 || !(fp.getHname().equals(prev.getHname()))) {
! System.out.println("New block " + Math.abs(dist1 - dist2) + " " + minStart + " " + prev.getHname());
SeqFeature sf1 = new SeqFeature(minStart ,maxStart ,"synten");
***************
*** 696,699 ****
--- 677,683 ----
if (fp.getLow() < minStart) {
minStart = fp.getLow();
+ if (minStart == 7665127) {
+ System.out.println("Restting minStart 2 " + fp.getHname());
+ }
}
if (fp.getHLow() < minHStart) {
***************
*** 1122,1125 ****
--- 1106,1111 ----
public void setLinks(FeatureSetI links){
this.links = groupLinks(links, maxDist);
+
+ System.out.println("Links " + this.links.size());
}
Index: SyntenyPanel.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/gui/SyntenyPanel.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** SyntenyPanel.java 13 Feb 2003 16:46:51 -0000 1.4
--- SyntenyPanel.java 27 Feb 2003 17:44:58 -0000 1.5
***************
*** 173,177 ****
setSize(700,700);
}
!
public static void main(String[] args) {
CurationSet set1 = null;
--- 173,177 ----
setSize(700,700);
}
! */
public static void main(String[] args) {
CurationSet set1 = null;
***************
*** 184,192 ****
int panel = Integer.parseInt(args[6]);
- try {
- GFFAdapter gff1 = new GFFAdapter(args[0]);
- GFFAdapter gff2 = new GFFAdapter(args[1]);
GFFFile gff3 = new GFFFile(args[2],"File");
--- 184,194 ----
int panel = Integer.parseInt(args[6]);
+ try {
+ GFFAdapter gff1 = new GFFAdapter();
+ GFFAdapter gff2 = new GFFAdapter();
+ gff1.setFilename(args[0]);
+ gff2.setFilename(args[1]);
GFFFile gff3 = new GFFFile(args[2],"File");
***************
*** 219,222 ****
--- 221,225 ----
ap1 = new StrandedZoomableApolloPanel(true,true,BorderLayout.NORTH,con1);
ap2 = new StrandedZoomableApolloPanel(true,true,BorderLayout.SOUTH,con2);
+
ap1.setSelectionManager(new SelectionManager());
ap2.setSelectionManager(new SelectionManager());
***************
*** 260,263 ****
--- 263,269 ----
SyntenyLinkPanel lp = new SyntenyLinkPanel(set3,maxDist,minSize,ap1.getTransformer(),ap2.getTransformer(),group,ap1,ap2);
+
+ lp.setLinks(set3);
+
Vector panels = new Vector();
panels.addElement(ap1);
***************
*** 268,273 ****
SyntenyPanel sp = new SyntenyPanel(panels,links);
-
-
sp.setPreferredSize(new Dimension(700,700));
--- 274,277 ----
***************
*** 322,329 ****
} else {
SyntenyLinkPanel lp = new SyntenyLinkPanel(set3,maxDist,minSize,null,null,group,null,null);
System.exit(0);
}
}
- */
public void setVisible(boolean state) {
super.setVisible(state);
--- 326,333 ----
} else {
SyntenyLinkPanel lp = new SyntenyLinkPanel(set3,maxDist,minSize,null,null,group,null,null);
+ lp.setLinks(set3);
System.exit(0);
}
}
public void setVisible(boolean state) {
super.setVisible(state);
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