X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=9a15e109c841164e69830f47ad36e5c12f97f45d;hb=30133ea9afab31009432eb013c299eb6c36ae75e;hp=10f4c6e02e89be2c515153d2e0a3a62fdf492c80;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git
diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 10f4c6e..9a15e10 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -1,19 +1,21 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* 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.
+ * 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.appletgui;
@@ -56,8 +58,6 @@ public class AlignViewport extends AlignmentViewport implements
boolean renderGaps = true;
- boolean showSequenceFeatures = false;
-
boolean showAnnotation = true;
boolean upperCasebold = false;
@@ -84,16 +84,10 @@ public class AlignViewport extends AlignmentViewport implements
boolean scaleRightWrapped = true;
- // The following vector holds the features which are
- // currently visible, in the correct order or rendering
- public Hashtable featuresDisplayed;
-
boolean showHiddenMarkers = true;
public jalview.bin.JalviewLite applet;
- Hashtable sequenceColours;
-
boolean MAC = false;
Stack historyList = new Stack();
@@ -256,16 +250,6 @@ public class AlignViewport extends AlignmentViewport implements
}
- public void showSequenceFeatures(boolean b)
- {
- showSequenceFeatures = b;
- }
-
- public boolean getShowSequenceFeatures()
- {
- return showSequenceFeatures;
- }
-
/**
* get the consensus sequence as displayed under the PID consensus annotation
* row.
@@ -486,26 +470,6 @@ public class AlignViewport extends AlignmentViewport implements
}
}
- public void setThreshold(int thresh)
- {
- threshold = thresh;
- }
-
- public int getThreshold()
- {
- return threshold;
- }
-
- public void setIncrement(int inc)
- {
- increment = inc;
- }
-
- public int getIncrement()
- {
- return increment;
- }
-
public void resetSeqLimits(int height)
{
setEndSeq(height / getCharHeight());
@@ -593,35 +557,6 @@ public class AlignViewport extends AlignmentViewport implements
showHiddenMarkers = show;
}
- public Color getSequenceColour(SequenceI seq)
- {
- if (sequenceColours == null || !sequenceColours.containsKey(seq))
- {
- return Color.white;
- }
- else
- {
- return (Color) sequenceColours.get(seq);
- }
- }
-
- public void setSequenceColour(SequenceI seq, Color col)
- {
- if (sequenceColours == null)
- {
- sequenceColours = new Hashtable();
- }
-
- if (col == null)
- {
- sequenceColours.remove(seq);
- }
- else
- {
- sequenceColours.put(seq, col);
- }
- }
-
boolean centreColumnLabels;
public boolean getCentreColumnLabels()
@@ -629,21 +564,6 @@ public class AlignViewport extends AlignmentViewport implements
return centreColumnLabels;
}
- public void updateSequenceIdColours()
- {
-
- for (SequenceGroup sg : alignment.getGroups())
- {
- if (sg.idColour != null)
- {
- for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
- {
- this.setSequenceColour(s, sg.idColour);
- }
- }
- }
- }
-
public boolean followHighlight = true;
public boolean getFollowHighlight()