X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=e11f1b484f1aea73fa822b58b35a3a61b64063df;hb=dfa04e77181fccfa6229ffef1591fc9c622d9b39;hp=244b650a13306cf81f8fe34282fdd638f9bce1e7;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git
diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
old mode 100755
new mode 100644
index 244b650..e11f1b4
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -1,19 +1,20 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
@@ -23,10 +24,10 @@ import java.awt.*;
import java.awt.event.*;
-import jalview.appletgui.FeatureSettings.MyCheckbox;
import jalview.datamodel.*;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.GraduatedColor;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
@@ -78,29 +79,41 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
}
}
- public void transferSettings(FeatureRenderer fr)
+ public void transferSettings(jalview.api.FeatureRenderer _fr)
{
- renderOrder = fr.renderOrder;
- featureGroups = fr.featureGroups;
- featureColours = fr.featureColours;
- transparency = fr.transparency;
- if (av!=null && fr.av!=null && fr.av!=av)
+ if (_fr instanceof FeatureRenderer)
{
- if (fr.av.featuresDisplayed!=null)
+ FeatureRenderer fr = (FeatureRenderer) _fr;
+ renderOrder = fr.renderOrder;
+ featureGroups = fr.featureGroups;
+ featureColours = fr.featureColours;
+ transparency = fr.transparency;
+ if (av != null && fr.av != null && fr.av != av)
{
- if (av.featuresDisplayed==null)
+ if (fr.av.featuresDisplayed != null)
{
- av.featuresDisplayed = new Hashtable();
- } else {
- av.featuresDisplayed.clear();
- }
- Enumeration en=fr.av.featuresDisplayed.keys();
- while (en.hasMoreElements())
- {
- av.featuresDisplayed.put(en.nextElement(), Boolean.TRUE);
+ if (av.featuresDisplayed == null)
+ {
+ av.featuresDisplayed = new Hashtable();
+ }
+ else
+ {
+ av.featuresDisplayed.clear();
+ }
+ Enumeration en = fr.av.featuresDisplayed.keys();
+ while (en.hasMoreElements())
+ {
+ av.featuresDisplayed.put(en.nextElement(), Boolean.TRUE);
+ }
}
}
}
+ else
+ {
+ throw new Error(
+ "Implementation error: cannot port feature settings from implementation of type "
+ + _fr.getClass() + " to " + getClass());
+ }
}
static String lastFeatureAdded;
@@ -193,7 +206,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
g.setColor(Color.black);
Font f = new Font("Verdana", Font.PLAIN, 10);
g.setFont(f);
- g.drawString("Label", 0, 0);
+ g.drawString(MessageManager.getString("label.label"), 0, 0);
}
else
{
@@ -363,7 +376,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
}
else
{
- dialog.ok.setLabel("Amend");
+ dialog.ok.setLabel(MessageManager.getString("label.amend"));
dialog.buttonPanel.add(deleteButton, 1);
deleteButton.addActionListener(new ActionListener()
{
@@ -786,10 +799,10 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
av.featuresDisplayed = new Hashtable();
Vector allfeatures = new Vector();
minmax = new Hashtable();
-
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ AlignmentI alignment = av.getAlignment();
+ for (int i = 0; i < alignment.getHeight(); i++)
{
- SequenceFeature[] features = av.alignment.getSequenceAt(i)
+ SequenceFeature[] features = alignment.getSequenceAt(i)
.getSequenceFeatures();
if (features == null)
@@ -1064,9 +1077,9 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
for (int i = 0; i < toset.length; i++)
{
Object st = featureGroups.get(toset[i]);
+ featureGroups.put(toset[i], new Boolean(visible));
if (st != null)
{
- featureGroups.put(toset[i], new Boolean(visible));
rdrw = rdrw || (visible != ((Boolean) st).booleanValue());
}
}
@@ -1090,6 +1103,8 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
}
}
+ ArrayList hiddenGroups = new ArrayList();
+
/**
* analyse alignment for groups and hash tables (used to be embedded in
* FeatureSettings.setTableData)
@@ -1103,29 +1118,34 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
{
featureGroups = new Hashtable();
}
- Vector allFeatures = new Vector();
- Vector allGroups = new Vector();
+ hiddenGroups = new ArrayList();
+ hiddenGroups.addAll(featureGroups.keySet());
+ ArrayList allFeatures = new ArrayList();
+ ArrayList allGroups = new ArrayList();
SequenceFeature[] tmpfeatures;
String group;
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ AlignmentI alignment = av.getAlignment();
+ for (int i = 0; i < alignment.getHeight(); i++)
{
- if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
+ if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
{
continue;
}
alignmentHasFeatures = true;
- tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
+ tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
int index = 0;
while (index < tmpfeatures.length)
{
if (tmpfeatures[index].getFeatureGroup() != null)
{
group = tmpfeatures[index].featureGroup;
+ // Remove group from the hiddenGroup list
+ hiddenGroups.remove(group);
if (!allGroups.contains(group))
{
- allGroups.addElement(group);
+ allGroups.add(group);
boolean visible = true;
if (featureGroups.containsKey(group))
@@ -1141,7 +1161,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
if (!allFeatures.contains(tmpfeatures[index].getType()))
{
- allFeatures.addElement(tmpfeatures[index].getType());
+ allFeatures.add(tmpfeatures[index].getType());
}
index++;
}
@@ -1170,16 +1190,17 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
Vector allFeatures = new Vector();
SequenceFeature[] tmpfeatures;
String group;
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ AlignmentI alignment = av.getAlignment();
+ for (int i = 0; i < alignment.getHeight(); i++)
{
- if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
+ if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
{
continue;
}
alignmentHasFeatures = true;
- tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
+ tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
int index = 0;
while (index < tmpfeatures.length)
{