X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=69695130904947cf654696d84dec5fd4e2330338;hb=d305e02d8b425bb501141ad32142aeb8572adc57;hp=e9829bb7d31ce7d454483915e0fd43cad1f5d7a4;hpb=2f4f1d8fb6878271b64f327bc58c895f458137af;p=jalview.git
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index e9829bb..6969513 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/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.
*/
/*
@@ -36,6 +38,7 @@
*/
package jalview.gui;
+import jalview.analysis.AnnotationSorter.SortOrder;
import jalview.analysis.NJTree;
import jalview.api.AlignViewportI;
import jalview.bin.Cache;
@@ -97,6 +100,8 @@ public class AlignViewport extends AlignmentViewport implements
boolean showAnnotation = true;
+ SortOrder sortAnnotationsBy = null;
+
int charHeight;
int charWidth;
@@ -356,12 +361,14 @@ public class AlignViewport extends AlignmentViewport implements
}
}
- wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
- showUnconserved = jalview.bin.Cache.getDefault("SHOW_UNCONSERVED",
+ wrapAlignment = Cache.getDefault("WRAP_ALIGNMENT", false);
+ showUnconserved = Cache.getDefault("SHOW_UNCONSERVED",
false);
- sortByTree = jalview.bin.Cache.getDefault("SORT_BY_TREE", false);
- followSelection = jalview.bin.Cache.getDefault("FOLLOW_SELECTIONS",
+ sortByTree = Cache.getDefault("SORT_BY_TREE", false);
+ followSelection = Cache.getDefault("FOLLOW_SELECTIONS",
true);
+ sortAnnotationsBy = SortOrder.valueOf(Cache.getDefault(
+ "SORT_ANNOTATIONS", SortOrder.SEQUENCE_AND_TYPE.name()));
}
/**
@@ -967,8 +974,10 @@ public class AlignViewport extends AlignmentViewport implements
{
// TODO: JAL-1126
if (historyList == null || redoList == null)
+ {
return new long[]
{ -1, -1 };
+ }
return new long[]
{ historyList.hashCode(), this.redoList.hashCode() };
}
@@ -1014,7 +1023,6 @@ public class AlignViewport extends AlignmentViewport implements
centreColumnLabels = centrecolumnlabels;
}
-
/**
* enable or disable the display of Database Cross References in the sequence
* ID tooltip
@@ -1206,7 +1214,9 @@ public class AlignViewport extends AlignmentViewport implements
Vector pdbs = alignment.getSequenceAt(i).getDatasetSequence()
.getPDBId();
if (pdbs == null)
+ {
continue;
+ }
SequenceI sq;
for (int p = 0; p < pdbs.size(); p++)
{
@@ -1214,7 +1224,9 @@ public class AlignViewport extends AlignmentViewport implements
if (p1.getId().equals(pdb.getId()))
{
if (!seqs.contains(sq = alignment.getSequenceAt(i)))
+ {
seqs.add(sq);
+ }
continue;
}
@@ -1263,4 +1275,14 @@ public class AlignViewport extends AlignmentViewport implements
Cache.log.debug("trigger update for " + calcId);
}
}
+
+ protected SortOrder getSortAnnotationsBy()
+ {
+ return sortAnnotationsBy;
+ }
+
+ protected void setSortAnnotationsBy(SortOrder sortAnnotationsBy)
+ {
+ this.sortAnnotationsBy = sortAnnotationsBy;
+ }
}