X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FRNAHelicesColourChooser.java;h=9809fa9a0223f0bd3b030faad72e1bd963d6c6e5;hb=a7169b1c72607f3c9357195b4999869650a2a891;hp=e575b91dc058277b63fce6e632ade28bfad0ab1a;hpb=44f6e9fd1e6df7c78950ef2c778e86add4ec498e;p=jalview.git
diff --git a/src/jalview/schemes/RNAHelicesColourChooser.java b/src/jalview/schemes/RNAHelicesColourChooser.java
index e575b91..9809fa9 100644
--- a/src/jalview/schemes/RNAHelicesColourChooser.java
+++ b/src/jalview/schemes/RNAHelicesColourChooser.java
@@ -1,92 +1,97 @@
/*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
- *
+ * 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 .
+ * 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.gui;
+package jalview.schemes;
-import java.util.*;
-import java.awt.event.*;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import java.util.Hashtable;
+import java.util.Map;
+import java.util.Vector;
/**
* Helps generate the colors for RNA secondary structure. Future: add option to
* change colors based on covariation.
*
* @author Lauren Michelle Lui
- *
+ * @deprecated this seems to be unfinished - just use RNAHelicesColour
*/
+@Deprecated
public class RNAHelicesColourChooser
{
- AlignViewport av;
+ AlignViewportI av;
- AlignmentPanel ap;
+ AlignmentViewPanel ap;
ColourSchemeI oldcs;
- Hashtable oldgroupColours;
+ Map oldgroupColours;
- jalview.datamodel.AlignmentAnnotation currentAnnotation;
+ AlignmentAnnotation currentAnnotation;
boolean adjusting = false;
- public RNAHelicesColourChooser(AlignViewport av, final AlignmentPanel ap)
+ public RNAHelicesColourChooser(AlignViewportI av,
+ final AlignmentViewPanel ap)
{
oldcs = av.getGlobalColourScheme();
if (av.getAlignment().getGroups() != null)
{
- oldgroupColours = new Hashtable();
- Vector allGroups = ap.av.getAlignment().getGroups();
- SequenceGroup sg;
- for (int g = 0; g < allGroups.size(); g++)
+ oldgroupColours = new Hashtable<>();
+ for (SequenceGroup sg : ap.getAlignment().getGroups())
{
- sg = (SequenceGroup) allGroups.get(g);
- if (sg.cs != null)
+ if (sg.getColourScheme() != null)
{
- oldgroupColours.put(sg, sg.cs);
+ oldgroupColours.put(sg, sg.getColourScheme());
}
}
}
this.av = av;
this.ap = ap;
- if (oldcs instanceof RNAHelicesColour)
- {
- RNAHelicesColour rhc = (RNAHelicesColour) oldcs;
-
- }
-
adjusting = true;
- Vector list = new Vector();
+ Vector list = new Vector<>();
int index = 1;
- for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+ AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
+ if (anns != null)
{
- String label = av.getAlignment().getAlignmentAnnotation()[i].label;
- if (!list.contains(label))
- list.addElement(label);
- else
- list.addElement(label + "_" + (index++));
+ for (int i = 0; i < anns.length; i++)
+ {
+ String label = anns[i].label;
+ if (!list.contains(label))
+ {
+ list.addElement(label);
+ }
+ else
+ {
+ list.addElement(label + "_" + (index++));
+ }
+ }
}
adjusting = false;
-
changeColour();
-
}
void changeColour()
@@ -96,54 +101,10 @@ public class RNAHelicesColourChooser
{
return;
}
-
- currentAnnotation = av.getAlignment().getAlignmentAnnotation()[0];// annotations.getSelectedIndex()];
-
- RNAHelicesColour rhc = null;
-
- rhc = new RNAHelicesColour(currentAnnotation);
+ RNAHelicesColour rhc = new RNAHelicesColour(av.getAlignment());
av.setGlobalColourScheme(rhc);
- if (av.getAlignment().getGroups() != null)
- {
- Vector allGroups = ap.av.getAlignment().getGroups();
- SequenceGroup sg;
- for (int g = 0; g < allGroups.size(); g++)
- {
- sg = (SequenceGroup) allGroups.get(g);
-
- if (sg.cs == null)
- {
- continue;
- }
-
- sg.cs = new RNAHelicesColour(currentAnnotation);
-
- }
- }
-
- ap.paintAlignment(false);
- }
-
- void reset()
- {
- av.setGlobalColourScheme(oldcs);
- if (av.getAlignment().getGroups() != null)
- {
- Vector allGroups = ap.av.getAlignment().getGroups();
- SequenceGroup sg;
- for (int g = 0; g < allGroups.size(); g++)
- {
- sg = (SequenceGroup) allGroups.get(g);
- sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
- }
- }
+ ap.paintAlignment(true, true);
}
-
- public void annotations_actionPerformed(ActionEvent e)
- {
- changeColour();
- }
-
}