git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
added description of alignment quality scores and separated
[jalview.git]
/
src
/
MCview
/
AppletPDBCanvas.java
diff --git
a/src/MCview/AppletPDBCanvas.java
b/src/MCview/AppletPDBCanvas.java
index
d91d43e
..
dc4cf0b
100755
(executable)
--- a/
src/MCview/AppletPDBCanvas.java
+++ b/
src/MCview/AppletPDBCanvas.java
@@
-118,7
+118,7
@@
public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
((PDBChain) pdb.chains.elementAt(i)).sequence, "pep");
\r
as.calcScoreMatrix();
\r
as.traceAlignment();
\r
((PDBChain) pdb.chains.elementAt(i)).sequence, "pep");
\r
as.calcScoreMatrix();
\r
as.traceAlignment();
\r
- PrintStream ps = new PrintStream(System.out)
\r
+ PrintStream ps = new PrintStream(System.out)
\r
{
\r
public void print(String x) {
\r
mappingDetails.append(x);
\r
{
\r
public void print(String x) {
\r
mappingDetails.append(x);
\r
@@
-498,8
+498,8
@@
public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
tmp.startCol = seqcanvas.getSequenceRenderer().
\r
getResidueBoxColour( sequence, index);
\r
\r
tmp.startCol = seqcanvas.getSequenceRenderer().
\r
getResidueBoxColour( sequence, index);
\r
\r
- // tmp.startCol = seqcanvas.getFeatureRenderer().
\r
- // findFeatureColour(tmp.startCol, sequence, index);
\r
+ tmp.startCol = seqcanvas.getFeatureRenderer().
\r
+ findFeatureColour(tmp.startCol, sequence, index);
\r
}
\r
}
\r
\r
}
\r
}
\r
\r
@@
-509,8
+509,8
@@
public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
{
\r
tmp.endCol = seqcanvas.getSequenceRenderer().
\r
getResidueBoxColour( sequence, index);
\r
{
\r
tmp.endCol = seqcanvas.getSequenceRenderer().
\r
getResidueBoxColour( sequence, index);
\r
- // tmp.endCol = seqcanvas.getFeatureRenderer().
\r
- // findFeatureColour(tmp.endCol, sequence, index);
\r
+ tmp.endCol = seqcanvas.getFeatureRenderer().
\r
+ findFeatureColour(tmp.endCol, sequence, index);
\r
}
\r
}
\r
}
\r
}
\r
}
\r
}
\r
@@
-716,35
+716,24
@@
public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
\r
void highlightSeqcanvas(int pos)
\r
{
\r
\r
void highlightSeqcanvas(int pos)
\r
{
\r
- int index = seqcanvas.getViewport().getAlignment().findIndex(sequence);
\r
-
\r
- int size = pos==-1?0:3;
\r
-
\r
- if(highlightRes!=null)
\r
- size += highlightRes.size()*3;
\r
-
\r
- int [] array = new int[size];
\r
- int i=0;
\r
+ SearchResults searchResults = new SearchResults();
\r
if(highlightRes!=null)
\r
{
\r
if(highlightRes!=null)
\r
{
\r
- for (i = 0; i < highlightRes.size(); i++)
\r
+ for (int i = 0; i < highlightRes.size(); i++)
\r
{
\r
int a = Integer.parseInt(highlightRes.elementAt(
\r
i).toString())+1;
\r
{
\r
int a = Integer.parseInt(highlightRes.elementAt(
\r
i).toString())+1;
\r
- array[i * 3] = index;
\r
- array[ (i * 3) + 1] = a;
\r
- array[ (i * 3) + 2] = a;
\r
+
\r
+ searchResults.addResult(sequence, a, a);
\r
}
\r
}
\r
\r
if(pos!=-1)
\r
{
\r
}
\r
}
\r
\r
if(pos!=-1)
\r
{
\r
- array[i * 3] = index;
\r
- array[i * 3 + 1] = pos+1;
\r
- array[i * 3 + 2] = pos+1;
\r
+ searchResults.addResult(sequence, pos+1, pos+1);
\r
}
\r
\r
}
\r
\r
- seqcanvas.highlightSearchResults(array);
\r
+ seqcanvas.highlightSearchResults(searchResults);
\r
}
\r
\r
\r
}
\r
\r
\r