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[jalview.git]
/
src
/
MCview
/
AppletPDBCanvas.java
diff --git
a/src/MCview/AppletPDBCanvas.java
b/src/MCview/AppletPDBCanvas.java
index
346ae1e
..
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
@@
-363,7
+363,8
@@
public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
g.drawString("Error loading PDB data!!", 50, getSize().height/2);
\r
return;
\r
}
\r
g.drawString("Error loading PDB data!!", 50, getSize().height/2);
\r
return;
\r
}
\r
- else if( !seqColoursReady )
\r
+
\r
+ if( !seqColoursReady )
\r
{
\r
g.setColor(Color.black);
\r
g.setFont(new Font("Verdana", Font.BOLD, 14));
\r
{
\r
g.setColor(Color.black);
\r
g.setFont(new Font("Verdana", Font.BOLD, 14));
\r
@@
-417,7
+418,13
@@
public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
drawLabels(ig);
\r
}
\r
\r
drawLabels(ig);
\r
}
\r
\r
-
\r
+ void setColours(jalview.schemes.ColourSchemeI cs)
\r
+ {
\r
+ bysequence = false;
\r
+ pdb.setColours(cs);
\r
+ redrawneeded = true;
\r
+ repaint();
\r
+ }
\r
public void updateSeqColours()
\r
{
\r
if (pdbAction)
\r
public void updateSeqColours()
\r
{
\r
if (pdbAction)
\r
@@
-491,8
+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
@@
-502,8
+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
@@
-709,35
+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
@@
-928,6
+924,8
@@
public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
\r
public void highlightRes(int ii)
\r
{
\r
\r
public void highlightRes(int ii)
\r
{
\r
+ if(!seqColoursReady)
\r
+ return;
\r
\r
if (highlightRes != null
\r
&& highlightRes.contains((ii-1) + ""))
\r
\r
if (highlightRes != null
\r
&& highlightRes.contains((ii-1) + ""))
\r