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javadoc
[jalview.git]
/
src
/
jalview
/
gui
/
FeatureSettings.java
diff --git
a/src/jalview/gui/FeatureSettings.java
b/src/jalview/gui/FeatureSettings.java
index
fae5259
..
1928382
100755
(executable)
--- a/
src/jalview/gui/FeatureSettings.java
+++ b/
src/jalview/gui/FeatureSettings.java
@@
-1,6
+1,6
@@
/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-19,11
+19,10
@@
package jalview.gui;
import java.io.*;
import java.util.*;
import java.io.*;
import java.util.*;
+import java.util.List;
import java.awt.*;
import java.awt.event.*;
import java.awt.*;
import java.awt.event.*;
-import java.awt.geom.AffineTransform;
-import java.awt.image.BufferedImage;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
@@
-38,6
+37,7
@@
import jalview.datamodel.*;
import jalview.io.*;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.GraduatedColor;
import jalview.io.*;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.GraduatedColor;
+import jalview.ws.dbsources.das.api.jalviewSourceI;
public class FeatureSettings extends JPanel
{
public class FeatureSettings extends JPanel
{
@@
-313,15
+313,15
@@
public class FeatureSettings extends JPanel
Vector allGroups = new Vector();
SequenceFeature[] tmpfeatures;
String group;
Vector allGroups = new Vector();
SequenceFeature[] tmpfeatures;
String group;
- for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
+ for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
{
{
- if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence()
+ if (af.getViewport().getAlignment().getSequenceAt(i).getDatasetSequence()
.getSequenceFeatures() == null)
{
continue;
}
.getSequenceFeatures() == null)
{
continue;
}
- tmpfeatures = af.getViewport().alignment.getSequenceAt(i)
+ tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
.getDatasetSequence().getSequenceFeatures();
int index = 0;
.getDatasetSequence().getSequenceFeatures();
int index = 0;
@@
-442,10
+442,10
@@
public class FeatureSettings extends JPanel
// Find out which features should be visible depending on which groups
// are selected / deselected
// and recompute average width ordering
// Find out which features should be visible depending on which groups
// are selected / deselected
// and recompute average width ordering
- for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
+ for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
{
{
- tmpfeatures = af.getViewport().alignment.getSequenceAt(i)
+ tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
.getDatasetSequence().getSequenceFeatures();
if (tmpfeatures == null)
{
.getDatasetSequence().getSequenceFeatures();
if (tmpfeatures == null)
{
@@
-714,13
+714,13
@@
public class FeatureSettings extends JPanel
PrintWriter out = new PrintWriter(new OutputStreamWriter(
new FileOutputStream(choice), "UTF-8"));
PrintWriter out = new PrintWriter(new OutputStreamWriter(
new FileOutputStream(choice), "UTF-8"));
- Enumeration e = fr.featureColours.keys();
+ Iterator e = fr.featureColours.keySet().iterator();
float[] sortOrder = new float[fr.featureColours.size()];
String[] sortTypes = new String[fr.featureColours.size()];
int i = 0;
float[] sortOrder = new float[fr.featureColours.size()];
String[] sortTypes = new String[fr.featureColours.size()];
int i = 0;
- while (e.hasMoreElements())
+ while (e.hasNext())
{
{
- sortTypes[i] = e.nextElement().toString();
+ sortTypes[i] = e.next().toString();
sortOrder[i] = fr.getOrder(sortTypes[i]);
i++;
}
sortOrder[i] = fr.getOrder(sortTypes[i]);
i++;
}
@@
-1134,13
+1134,13
@@
public class FeatureSettings extends JPanel
if (fr.featureGroups != null)
{
if (fr.featureGroups != null)
{
- Enumeration en = fr.featureGroups.keys();
+ Iterator en = fr.featureGroups.keySet().iterator();
gps = new String[fr.featureColours.size()];
int g = 0;
boolean valid = false;
gps = new String[fr.featureColours.size()];
int g = 0;
boolean valid = false;
- while (en.hasMoreElements())
+ while (en.hasNext())
{
{
- String gp = (String) en.nextElement();
+ String gp = (String) en.next();
Boolean on = (Boolean) fr.featureGroups.get(gp);
if (on != null && on.booleanValue())
{
Boolean on = (Boolean) fr.featureGroups.get(gp);
if (on != null && on.booleanValue())
{
@@
-1177,7
+1177,7
@@
public class FeatureSettings extends JPanel
* @param checkDbRefs
* @param promptFetchDbRefs
*/
* @param checkDbRefs
* @param promptFetchDbRefs
*/
- private void doDasFeatureFetch(Vector selectedSources,
+ private void doDasFeatureFetch(List<jalviewSourceI> selectedSources,
boolean checkDbRefs, boolean promptFetchDbRefs)
{
SequenceI[] dataset, seqs;
boolean checkDbRefs, boolean promptFetchDbRefs)
{
SequenceI[] dataset, seqs;
@@
-1225,9
+1225,9
@@
public class FeatureSettings extends JPanel
* Vector of Strings to resolve to DAS source nicknames.
* @return sources that are present in source list.
*/
* Vector of Strings to resolve to DAS source nicknames.
* @return sources that are present in source list.
*/
- public Vector resolveSourceNicknames(Vector sources)
+ public List<jalviewSourceI> resolveSourceNicknames(Vector sources)
{
{
- return dassourceBrowser.resolveSourceNicknames(sources);
+ return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources);
}
/**
}
/**
@@
-1253,14
+1253,14
@@
public class FeatureSettings extends JPanel
public void fetchDasFeatures(Vector sources, boolean block)
{
initDasSources();
public void fetchDasFeatures(Vector sources, boolean block)
{
initDasSources();
- Vector resolved = resolveSourceNicknames(sources);
+ List<jalviewSourceI> resolved = dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources);
if (resolved.size() == 0)
{
resolved = dassourceBrowser.getSelectedSources();
}
if (resolved.size() > 0)
{
if (resolved.size() == 0)
{
resolved = dassourceBrowser.getSelectedSources();
}
if (resolved.size() > 0)
{
- final Vector dassources = resolved;
+ final List<jalviewSourceI> dassources = resolved;
fetchDAS.setEnabled(false);
// cancelDAS.setEnabled(true); doDasFetch does this.
Runnable fetcher = new Runnable()
fetchDAS.setEnabled(false);
// cancelDAS.setEnabled(true); doDasFetch does this.
Runnable fetcher = new Runnable()