X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=10e14d1cea538671b4af2c6791726959df4ae339;hb=1f8022f2b026e9852c76f0803d92da016a1bde5e;hp=de8f310cf7b8b3f90de225275a725bd21741f184;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index de8f310..10e14d1 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 2.8.1)
+ * 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.
*/
/*
@@ -36,12 +38,12 @@
*/
package jalview.gui;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.NJTree;
import jalview.api.AlignViewportI;
import jalview.bin.Cache;
-import jalview.datamodel.AlignmentAnnotation;
+import jalview.commands.CommandI;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
@@ -95,7 +97,9 @@ public class AlignViewport extends AlignmentViewport implements
boolean showSequenceFeatures = false;
- boolean showAnnotation = true;
+ private boolean showAnnotation = true;
+
+ SequenceAnnotationOrder sortAnnotationsBy = null;
int charHeight;
@@ -125,7 +129,7 @@ public class AlignViewport extends AlignmentViewport implements
* Keys are the feature types which are currently visible. Note: Values are
* not used!
*/
- Hashtable featuresDisplayed = null;
+ private Hashtable featuresDisplayed = null;
boolean antiAlias = false;
@@ -135,9 +139,9 @@ public class AlignViewport extends AlignmentViewport implements
boolean gatherViewsHere = false;
- Stack historyList = new Stack();
+ Stack historyList = new Stack();
- Stack redoList = new Stack();
+ Stack redoList = new Stack();
int thresholdTextColour = 0;
@@ -145,8 +149,9 @@ public class AlignViewport extends AlignmentViewport implements
Color textColour2 = Color.white;
- boolean rightAlignIds = false;
+ private boolean rightAlignIds = false;
+ private AnnotationColumnSelection currentAnnotationColumnSelectionState;
/**
* Creates a new AlignViewport object.
*
@@ -282,9 +287,9 @@ public class AlignViewport extends AlignmentViewport implements
antiAlias = Cache.getDefault("ANTI_ALIAS", false);
showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
- showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
+ setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
- rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
+ setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false);
autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
@@ -332,10 +337,6 @@ public class AlignViewport extends AlignmentViewport implements
false);
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
- consensus = new AlignmentAnnotation("Consensus", "PID",
- new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
- consensus.hasText = true;
- consensus.autoCalculated = true;
}
initAutoAnnotation();
if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
@@ -356,12 +357,15 @@ public class AlignViewport extends AlignmentViewport implements
}
}
- wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
- showUnconserved = jalview.bin.Cache.getDefault("SHOW_UNCONSERVED",
- false);
- sortByTree = jalview.bin.Cache.getDefault("SORT_BY_TREE", false);
- followSelection = jalview.bin.Cache.getDefault("FOLLOW_SELECTIONS",
- true);
+ wrapAlignment = Cache.getDefault("WRAP_ALIGNMENT", false);
+ showUnconserved = Cache.getDefault("SHOW_UNCONSERVED", false);
+ sortByTree = Cache.getDefault("SORT_BY_TREE", false);
+ followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true);
+ sortAnnotationsBy = SequenceAnnotationOrder.valueOf(Cache.getDefault(
+ Preferences.SORT_ANNOTATIONS,
+ SequenceAnnotationOrder.NONE.name()));
+ showAutocalculatedAbove = Cache.getDefault(
+ Preferences.SHOW_AUTOCALC_ABOVE, false);
}
/**
@@ -836,7 +840,7 @@ public class AlignViewport extends AlignmentViewport implements
*/
public boolean getShowAnnotation()
{
- return showAnnotation;
+ return isShowAnnotation();
}
/**
@@ -967,8 +971,10 @@ 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 +1020,6 @@ public class AlignViewport extends AlignmentViewport implements
centreColumnLabels = centrecolumnlabels;
}
-
/**
* enable or disable the display of Database Cross References in the sequence
* ID tooltip
@@ -1206,7 +1211,9 @@ 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 +1221,9 @@ public class AlignViewport extends AlignmentViewport implements
if (p1.getId().equals(pdb.getId()))
{
if (!seqs.contains(sq = alignment.getSequenceAt(i)))
+ {
seqs.add(sq);
+ }
continue;
}
@@ -1246,6 +1255,8 @@ public class AlignViewport extends AlignmentViewport implements
private Hashtable calcIdParams = new Hashtable();
+ private boolean showAutocalculatedAbove;
+
public AutoCalcSetting getCalcIdSettingsFor(String calcId)
{
return calcIdParams.get(calcId);
@@ -1263,4 +1274,60 @@ public class AlignViewport extends AlignmentViewport implements
Cache.log.debug("trigger update for " + calcId);
}
}
+
+
+ public Hashtable getFeaturesDisplayed()
+ {
+ return featuresDisplayed;
+ }
+
+ public void setFeaturesDisplayed(Hashtable featuresDisplayed)
+ {
+ this.featuresDisplayed = featuresDisplayed;
+ }
+ protected SequenceAnnotationOrder getSortAnnotationsBy()
+ {
+ return sortAnnotationsBy;
+ }
+
+ protected void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy)
+ {
+ this.sortAnnotationsBy = sortAnnotationsBy;
+ }
+
+ protected boolean isShowAutocalculatedAbove()
+ {
+ return showAutocalculatedAbove;
+ }
+
+ protected void setShowAutocalculatedAbove(boolean showAutocalculatedAbove)
+ {
+ this.showAutocalculatedAbove = showAutocalculatedAbove;
+ }
+
+ public boolean isShowAnnotation()
+ {
+ return showAnnotation;
+ }
+
+ public boolean isRightAlignIds()
+ {
+ return rightAlignIds;
+ }
+
+ public void setRightAlignIds(boolean rightAlignIds)
+ {
+ this.rightAlignIds = rightAlignIds;
+ }
+
+ public AnnotationColumnSelection getCurrentAnnotationColumnSelectionState()
+ {
+ return currentAnnotationColumnSelectionState;
+ }
+
+ public void setCurrentAnnotationColumnSelectionState(
+ AnnotationColumnSelection currentAnnotationColumnSelectionState)
+ {
+ this.currentAnnotationColumnSelectionState = currentAnnotationColumnSelectionState;
+ }
}