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Add new feature from seqrch results
author
amwaterhouse
<Andrew Waterhouse>
Thu, 16 Mar 2006 15:13:55 +0000
(15:13 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Thu, 16 Mar 2006 15:13:55 +0000
(15:13 +0000)
src/jalview/appletgui/Finder.java
patch
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diff --git
a/src/jalview/appletgui/Finder.java
b/src/jalview/appletgui/Finder.java
index
fb8c280
..
8905b52
100755
(executable)
--- a/
src/jalview/appletgui/Finder.java
+++ b/
src/jalview/appletgui/Finder.java
@@
-84,20
+84,37
@@
public class Finder extends Panel implements ActionListener
public void createNewGroup_actionPerformed()
\r
{
\r
\r
public void createNewGroup_actionPerformed()
\r
{
\r
\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, null);
\r
+ Dialog dialog = new Dialog(ap.alignFrame, "Enter New Feature Name", true);
\r
+ dialog.add(cap);
\r
+
\r
+ cap.setText(textfield.getText());
\r
+
\r
+ dialog.setBounds( frame.getLocation().x+frame.getSize().width+5,
\r
+ frame.getLocation().y+20,300,100);
\r
+ dialog.show();
\r
+
\r
+
\r
+ String featureName = cap.getText().trim();
\r
+ if(featureName.length()<1)
\r
+ return;
\r
+
\r
+
\r
for (int i = 0; i < searchResults.getSize(); i ++ )
\r
{
\r
SequenceI seq = searchResults.getResultSequence(i);
\r
\r
for (int i = 0; i < searchResults.getSize(); i ++ )
\r
{
\r
SequenceI seq = searchResults.getResultSequence(i);
\r
\r
- SequenceFeature sf = new SequenceFeature(textfield.getText(),
\r
- "Search Results", null,
\r
+ SequenceFeature sf = new SequenceFeature(featureName,
\r
+ null, null,
\r
searchResults.getResultStart(i),
\r
searchResults.getResultEnd(i));
\r
\r
ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(
\r
searchResults.getResultStart(i),
\r
searchResults.getResultEnd(i));
\r
\r
ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(
\r
- textfield.getText(), new Color(60,160,115));
\r
+ featureName, new Color(60,160,115));
\r
seq.addSequenceFeature(sf);
\r
}
\r
\r
seq.addSequenceFeature(sf);
\r
}
\r
\r
+ ap.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures();
\r
ap.alignFrame.sequenceFeatures.setState(true);
\r
av.showSequenceFeatures(true);
\r
ap.highlightSearchResults(null);
\r
ap.alignFrame.sequenceFeatures.setState(true);
\r
av.showSequenceFeatures(true);
\r
ap.highlightSearchResults(null);
\r
@@
-155,6
+172,7
@@
public class Finder extends Panel implements ActionListener
\r
while (!found && seqIndex < end)
\r
{
\r
\r
while (!found && seqIndex < end)
\r
{
\r
+
\r
seq = (Sequence) av.alignment.getSequenceAt(seqIndex);
\r
\r
if (selection != null && !selection.sequences.contains(seq))
\r
seq = (Sequence) av.alignment.getSequenceAt(seqIndex);
\r
\r
if (selection != null && !selection.sequences.contains(seq))
\r
@@
-172,7
+190,7
@@
public class Finder extends Panel implements ActionListener
}
\r
\r
///Shall we ignore gaps????
\r
}
\r
\r
///Shall we ignore gaps????
\r
- StringBuffer noGaps = new StringBuffer();
\r
+ StringBuffer noGapsSB = new StringBuffer();
\r
int insertCount = 0;
\r
Vector spaces = new Vector();
\r
\r
int insertCount = 0;
\r
Vector spaces = new Vector();
\r
\r
@@
-181,7
+199,7
@@
public class Finder extends Panel implements ActionListener
\r
if (!jalview.util.Comparison.isGap(item.charAt(j)))
\r
{
\r
\r
if (!jalview.util.Comparison.isGap(item.charAt(j)))
\r
{
\r
- noGaps.append(item.charAt(j));
\r
+ noGapsSB.append(item.charAt(j));
\r
spaces.addElement(new Integer(insertCount));
\r
}
\r
else
\r
spaces.addElement(new Integer(insertCount));
\r
}
\r
else
\r
@@
-190,10
+208,12
@@
public class Finder extends Panel implements ActionListener
}
\r
}
\r
\r
}
\r
}
\r
\r
+ String noGaps = noGapsSB.toString();
\r
+
\r
for (int r = resIndex; r < noGaps.length(); r++)
\r
{
\r
\r
for (int r = resIndex; r < noGaps.length(); r++)
\r
{
\r
\r
- if (regex.searchFrom(noGaps.toString(), r))
\r
+ if (regex.searchFrom(noGaps, r))
\r
{
\r
resIndex = regex.matchedFrom();
\r
if (selection != null &&
\r
{
\r
resIndex = regex.matchedFrom();
\r
if (selection != null &&
\r
@@
-264,8
+284,8
@@
public class Finder extends Panel implements ActionListener
\r
if (findAll)
\r
{
\r
\r
if (findAll)
\r
{
\r
- String message = (searchResults.getSize()) + " matches found.";
\r
- System.out.println(message);
\r
+ String message = (searchResults==null?0 : searchResults.getSize()) + " matches found.";
\r
+ ap.alignFrame.statusBar.setText("Search results: "+searchString+" : "+message);
\r
}
\r
\r
}
\r
}
\r
\r
}
\r