X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=8fc10d76fe26fa3b26106ded42b340de76ad6091;hb=373a0f23b37fdd3c40d3ebb4a3c9120f5773bb45;hp=26fb890708e91171dee946e211f8d38689ee5e85;hpb=1b3b9ada9b959de9d66b1d477bb155a0c6668c8e;p=jalview.git
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 26fb890..8fc10d7 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,19 +1,22 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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.
*/
/*
* Jalview - A Sequence Alignment Editor and Viewer
@@ -35,21 +38,42 @@
*/
package jalview.gui;
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-import jalview.api.StructureSelectionManagerProvider;
-
-import jalview.bin.*;
-
-import jalview.datamodel.*;
-
-import jalview.schemes.*;
+import jalview.analysis.AlignmentUtils;
+import jalview.analysis.AlignmentUtils.MappingResult;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.analysis.NJTree;
+import jalview.api.AlignViewportI;
+import jalview.api.ViewStyleI;
+import jalview.bin.Cache;
+import jalview.commands.CommandI;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.UserColourScheme;
+import jalview.structure.CommandListener;
import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.ws.params.AutoCalcSetting;
+
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Rectangle;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Set;
+import java.util.Vector;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
/**
* DOCUMENT ME!
@@ -57,10 +81,9 @@ import jalview.structure.VamsasSource;
* @author $author$
* @version $Revision: 1.141 $
*/
-public class AlignViewport implements SelectionSource, VamsasSource
+public class AlignViewport extends AlignmentViewport implements
+ SelectionSource, AlignViewportI, CommandListener
{
- private static final int RIGHT_JUSTIFY = 1;
-
int startRes;
int endRes;
@@ -69,130 +92,24 @@ public class AlignViewport implements SelectionSource, VamsasSource
int endSeq;
- boolean showJVSuffix = true;
-
- boolean showText = true;
-
- boolean showColourText = false;
-
- boolean showBoxes = true;
-
- boolean wrapAlignment = false;
-
- boolean renderGaps = true;
-
- boolean showSequenceFeatures = false;
-
- boolean showAnnotation = true;
- boolean colourAppliesToAllGroups = true;
-
- ColourSchemeI globalColourScheme = null;
-
- boolean conservationColourSelected = false;
-
- boolean abovePIDThreshold = false;
-
- SequenceGroup selectionGroup;
-
- int charHeight;
-
- int charWidth;
-
- boolean validCharWidth;
-
- int wrappedWidth;
+ SequenceAnnotationOrder sortAnnotationsBy = null;
Font font;
- boolean seqNameItalics;
-
- AlignmentI alignment;
-
- ColumnSelection colSel = new ColumnSelection();
-
- int threshold;
-
- int increment;
-
NJTree currentTree = null;
- boolean scaleAboveWrapped = false;
-
- boolean scaleLeftWrapped = true;
-
- boolean scaleRightWrapped = true;
-
- boolean hasHiddenColumns = false;
-
- boolean hasHiddenRows = false;
-
- boolean showHiddenMarkers = true;
-
boolean cursorMode = false;
- /**
- * Keys are the feature types which are currently visible. Note: Values are
- * not used!
- */
- Hashtable featuresDisplayed = null;
-
- /** DOCUMENT ME!! */
- public Hashtable[] hconsensus;
-
- AlignmentAnnotation consensus;
-
- AlignmentAnnotation conservation;
-
- AlignmentAnnotation quality;
-
- AlignmentAnnotation[] groupConsensus;
-
- AlignmentAnnotation[] groupConservation;
-
- boolean autoCalculateConsensus = true;
-
- /** DOCUMENT ME!! */
- public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
-
- // JBPNote Prolly only need this in the applet version.
- private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
- this);
-
- boolean ignoreGapsInConsensusCalculation = false;
-
- boolean isDataset = false;
-
boolean antiAlias = false;
- boolean padGaps = false;
-
- Rectangle explodedPosition;
+ private Rectangle explodedGeometry;
String viewName;
- String sequenceSetID;
-
- boolean gatherViewsHere = false;
-
- Stack historyList = new Stack();
-
- Stack redoList = new Stack();
-
- Hashtable sequenceColours;
-
- int thresholdTextColour = 0;
-
- Color textColour = Color.black;
-
- Color textColour2 = Color.white;
-
- boolean rightAlignIds = false;
-
- Hashtable hiddenRepSequences;
-
- boolean sortByTree;
+ private boolean gatherViewsHere = false;
+ private AnnotationColumnChooser annotationColumnSelectionState;
/**
* Creates a new AlignViewport object.
*
@@ -248,16 +165,7 @@ public class AlignViewport implements SelectionSource, VamsasSource
setAlignment(al);
if (hiddenColumns != null)
{
- this.colSel = hiddenColumns;
- if (hiddenColumns.getHiddenColumns() != null
- && hiddenColumns.getHiddenColumns().size() > 0)
- {
- hasHiddenColumns = true;
- }
- else
- {
- hasHiddenColumns = false;
- }
+ colSel = hiddenColumns;
}
init();
}
@@ -304,46 +212,51 @@ public class AlignViewport implements SelectionSource, VamsasSource
setAlignment(al);
if (hiddenColumns != null)
{
- this.colSel = hiddenColumns;
- if (hiddenColumns.getHiddenColumns() != null
- && hiddenColumns.getHiddenColumns().size() > 0)
- {
- hasHiddenColumns = true;
- }
- else
- {
- hasHiddenColumns = false;
- }
+ colSel = hiddenColumns;
}
init();
}
- void init()
+ private void applyViewProperties()
{
- this.startRes = 0;
- this.endRes = alignment.getWidth() - 1;
- this.startSeq = 0;
- this.endSeq = alignment.getHeight() - 1;
-
antiAlias = Cache.getDefault("ANTI_ALIAS", false);
- showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
- showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
+ viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true));
+ setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
- rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
- centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false);
+ setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
+ setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false));
autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
- padGaps = Cache.getDefault("PAD_GAPS", true);
- shownpfeats = Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true);
- showdbrefs = Cache.getDefault("SHOW_DBREFS_TOOLTIP", true);
+ setPadGaps(Cache.getDefault("PAD_GAPS", true));
+ setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
+ setShowDBRefs(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
+ viewStyle.setSeqNameItalics(Cache.getDefault("ID_ITALICS", true));
+ viewStyle.setWrapAlignment(Cache.getDefault("WRAP_ALIGNMENT", false));
+ viewStyle.setShowUnconserved(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);
+
+ }
+
+ void init()
+ {
+ this.startRes = 0;
+ this.endRes = alignment.getWidth() - 1;
+ this.startSeq = 0;
+ this.endSeq = alignment.getHeight() - 1;
+ applyViewProperties();
String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
String fontSize = Cache.getDefault("FONT_SIZE", "10");
- seqNameItalics = Cache.getDefault("ID_ITALICS", true);
-
int style = 0;
if (fontStyle.equals("bold"))
@@ -355,7 +268,7 @@ public class AlignViewport implements SelectionSource, VamsasSource
style = 2;
}
- setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
+ setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
alignment
.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
@@ -366,53 +279,20 @@ public class AlignViewport implements SelectionSource, VamsasSource
{
if (!alignment.isNucleotide())
{
- conservation = new AlignmentAnnotation("Conservation",
- "Conservation of total alignment less than " + ConsPercGaps
- + "% gaps", new Annotation[1], 0f, 11f,
- AlignmentAnnotation.BAR_GRAPH);
- conservation.hasText = true;
- conservation.autoCalculated = true;
-
- if (Cache.getDefault("SHOW_CONSERVATION", true))
- {
- alignment.addAnnotation(conservation);
- }
-
- if (Cache.getDefault("SHOW_QUALITY", true))
- {
- quality = new AlignmentAnnotation("Quality",
- "Alignment Quality based on Blosum62 scores",
- new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
- quality.hasText = true;
- quality.autoCalculated = true;
-
- alignment.addAnnotation(quality);
- }
+ showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
+ showQuality = Cache.getDefault("SHOW_QUALITY", true);
showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
false);
-
- {
-
- }
}
showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
true);
showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
+ normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
+ false);
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
- // TODO: add menu option action that nulls or creates consensus object
- // depending on if the user wants to see the annotation or not in a
- // specific alignment
- consensus = new AlignmentAnnotation("Consensus", "PID",
- new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
- consensus.hasText = true;
- consensus.autoCalculated = true;
-
- if (Cache.getDefault("SHOW_IDENTITY", true))
- {
- alignment.addAnnotation(consensus);
- }
+ showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
}
-
+ initAutoAnnotation();
if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
{
globalColourScheme = ColourSchemeProperty.getColour(alignment,
@@ -422,7 +302,7 @@ public class AlignViewport implements SelectionSource, VamsasSource
{
globalColourScheme = UserDefinedColours.loadDefaultColours();
((UserColourScheme) globalColourScheme).setThreshold(0,
- getIgnoreGapsConsensus());
+ isIgnoreGapsConsensus());
}
if (globalColourScheme != null)
@@ -430,179 +310,6 @@ public class AlignViewport implements SelectionSource, VamsasSource
globalColourScheme.setConsensus(hconsensus);
}
}
-
- 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);
- }
-
- /**
- * set the flag
- *
- * @param b
- * features are displayed if true
- */
- public void setShowSequenceFeatures(boolean b)
- {
- showSequenceFeatures = b;
- }
-
- public boolean getShowSequenceFeatures()
- {
- return showSequenceFeatures;
- }
-
- ConservationThread conservationThread;
-
- ConsensusThread consensusThread;
-
- boolean consUpdateNeeded = false;
-
- static boolean UPDATING_CONSENSUS = false;
-
- static boolean UPDATING_CONSERVATION = false;
-
- boolean updatingConsensus = false;
-
- boolean updatingConservation = false;
-
- /**
- * centre columnar annotation labels in displayed alignment annotation TODO:
- * add to jalviewXML and annotation display settings
- */
- boolean centreColumnLabels = false;
-
- private boolean showdbrefs;
-
- private boolean shownpfeats;
-
- /**
- * trigger update of conservation annotation
- */
- public void updateConservation(final AlignmentPanel ap)
- {
- // see note in mantis : issue number 8585
- if (alignment.isNucleotide() || conservation == null
- || !autoCalculateConsensus)
- {
- return;
- }
-
- conservationThread = new ConservationThread(this, ap);
- conservationThread.start();
- }
-
- /**
- * trigger update of consensus annotation
- */
- public void updateConsensus(final AlignmentPanel ap)
- {
- // see note in mantis : issue number 8585
- if (consensus == null || !autoCalculateConsensus)
- {
- return;
- }
- consensusThread = new ConsensusThread(ap);
- consensusThread.start();
- }
-
- class ConsensusThread extends Thread
- {
- AlignmentPanel ap;
-
- public ConsensusThread(AlignmentPanel ap)
- {
- this.ap = ap;
- }
-
- public void run()
- {
- updatingConsensus = true;
- while (UPDATING_CONSENSUS)
- {
- try
- {
- if (ap != null)
- {
- ap.paintAlignment(false);
- }
-
- Thread.sleep(200);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- UPDATING_CONSENSUS = true;
-
- try
- {
- int aWidth = (alignment != null) ? alignment.getWidth() : -1; // null
- // pointer
- // possibility
- // here.
- if (aWidth <= 0)
- {
- updatingConsensus = false;
- UPDATING_CONSENSUS = false;
- return;
- }
-
- consensus.annotations = null;
- consensus.annotations = new Annotation[aWidth];
-
- hconsensus = new Hashtable[aWidth];
- AAFrequency.calculate(alignment.getSequencesArray(), 0,
- alignment.getWidth(), hconsensus, true);
- updateAnnotation(true);
-
- if (globalColourScheme != null)
- {
- globalColourScheme.setConsensus(hconsensus);
- }
-
- } catch (OutOfMemoryError error)
- {
- alignment.deleteAnnotation(consensus);
-
- consensus = null;
- hconsensus = null;
- new OOMWarning("calculating consensus", error);
- }
- UPDATING_CONSENSUS = false;
- updatingConsensus = false;
-
- if (ap != null)
- {
- ap.paintAlignment(true);
- }
- }
-
- /**
- * update the consensus annotation from the sequence profile data using
- * current visualization settings.
- */
- public void updateAnnotation()
- {
- updateAnnotation(false);
- }
-
- protected void updateAnnotation(boolean immediate)
- {
- // TODO: make calls thread-safe, so if another thread calls this method,
- // it will either return or wait until one calculation is finished.
- if (immediate
- || (!updatingConsensus && consensus != null && hconsensus != null))
- {
- AAFrequency.completeConsensus(consensus, hconsensus, 0,
- hconsensus.length, ignoreGapsInConsensusCalculation,
- showSequenceLogo);
- }
- }
}
/**
@@ -644,66 +351,6 @@ public class AlignViewport implements SelectionSource, VamsasSource
}
/**
- *
- *
- * @return null or the currently selected sequence region
- */
- public SequenceGroup getSelectionGroup()
- {
- return selectionGroup;
- }
-
- /**
- * Set the selection group for this window.
- *
- * @param sg - group holding references to sequences in this alignment view
- *
- */
- public void setSelectionGroup(SequenceGroup sg)
- {
- selectionGroup = sg;
- }
-
- /**
- * GUI state
- * @return true if conservation based shading is enabled
- */
- public boolean getConservationSelected()
- {
- return conservationColourSelected;
- }
-
- /**
- * GUI state
- * @param b
- * enable conservation based shading
- */
- public void setConservationSelected(boolean b)
- {
- conservationColourSelected = b;
- }
-
- /**
- * GUI state
- * @return true if percent identity threshold is applied to shading
- */
- public boolean getAbovePIDThreshold()
- {
- return abovePIDThreshold;
- }
-
- /**
- * GUI state
- *
- *
- * @param b indicate if percent identity threshold is applied to shading
- */
- public void setAbovePIDThreshold(boolean b)
- {
- abovePIDThreshold = b;
- }
-
- /**
* DOCUMENT ME!
*
* @return DOCUMENT ME!
@@ -736,27 +383,6 @@ public class AlignViewport implements SelectionSource, VamsasSource
/**
* DOCUMENT ME!
*
- * @param cs
- * DOCUMENT ME!
- */
- public void setGlobalColourScheme(ColourSchemeI cs)
- {
- globalColourScheme = cs;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public ColourSchemeI getGlobalColourScheme()
- {
- return globalColourScheme;
- }
-
- /**
- * DOCUMENT ME!
- *
* @param res
* DOCUMENT ME!
*/
@@ -830,24 +456,44 @@ public class AlignViewport implements SelectionSource, VamsasSource
return endSeq;
}
+ boolean validCharWidth;
+
/**
- * DOCUMENT ME!
+ * update view settings with the given font. You may need to call
+ * alignPanel.fontChanged to update the layout geometry
*
- * @param f
- * DOCUMENT ME!
+ * @param setGrid
+ * when true, charWidth/height is set according to font mentrics
*/
- public void setFont(Font f)
+ public void setFont(Font f, boolean setGrid)
{
font = f;
Container c = new Container();
java.awt.FontMetrics fm = c.getFontMetrics(font);
- setCharHeight(fm.getHeight());
- setCharWidth(fm.charWidth('M'));
+ int w = viewStyle.getCharWidth(), ww = fm.charWidth('M'), h = viewStyle
+ .getCharHeight();
+ if (setGrid)
+ {
+ setCharHeight(fm.getHeight());
+ setCharWidth(ww);
+ }
+ viewStyle.setFontName(font.getName());
+ viewStyle.setFontStyle(font.getStyle());
+ viewStyle.setFontSize(font.getSize());
+
validCharWidth = true;
}
+ @Override
+ public void setViewStyle(ViewStyleI settingsForView)
+ {
+ super.setViewStyle(settingsForView);
+ setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
+ viewStyle.getFontSize()), false);
+
+ }
/**
* DOCUMENT ME!
*
@@ -861,12 +507,22 @@ public class AlignViewport implements SelectionSource, VamsasSource
/**
* DOCUMENT ME!
*
- * @param w
+ * @param align
* DOCUMENT ME!
*/
- public void setCharWidth(int w)
+ public void setAlignment(AlignmentI align)
{
- this.charWidth = w;
+ if (alignment != null && alignment.getCodonFrames() != null)
+ {
+ StructureSelectionManager.getStructureSelectionManager(
+ Desktop.instance).removeMappings(alignment.getCodonFrames());
+ }
+ this.alignment = align;
+ if (alignment != null && alignment.getCodonFrames() != null)
+ {
+ StructureSelectionManager.getStructureSelectionManager(
+ Desktop.instance).addMappings(alignment.getCodonFrames());
+ }
}
/**
@@ -874,955 +530,54 @@ public class AlignViewport implements SelectionSource, VamsasSource
*
* @return DOCUMENT ME!
*/
- public int getCharWidth()
+ public char getGapCharacter()
{
- return charWidth;
+ return getAlignment().getGapCharacter();
}
/**
* DOCUMENT ME!
*
- * @param h
+ * @param gap
* DOCUMENT ME!
*/
- public void setCharHeight(int h)
+ public void setGapCharacter(char gap)
{
- this.charHeight = h;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getCharHeight()
- {
- return charHeight;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param w
- * DOCUMENT ME!
- */
- public void setWrappedWidth(int w)
- {
- this.wrappedWidth = w;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getWrappedWidth()
- {
- return wrappedWidth;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public AlignmentI getAlignment()
- {
- return alignment;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param align
- * DOCUMENT ME!
- */
- public void setAlignment(AlignmentI align)
- {
- if (alignment != null && alignment.getCodonFrames() != null)
- {
- StructureSelectionManager.getStructureSelectionManager(Desktop.instance)
- .removeMappings(alignment.getCodonFrames());
- }
- this.alignment = align;
- if (alignment.getCodonFrames() != null)
- {
- StructureSelectionManager.getStructureSelectionManager(Desktop.instance).addMappings(
- alignment.getCodonFrames());
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param state
- * DOCUMENT ME!
- */
- public void setWrapAlignment(boolean state)
- {
- wrapAlignment = state;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param state
- * DOCUMENT ME!
- */
- public void setShowText(boolean state)
- {
- showText = state;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param state
- * DOCUMENT ME!
- */
- public void setRenderGaps(boolean state)
- {
- renderGaps = state;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getColourText()
- {
- return showColourText;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param state
- * DOCUMENT ME!
- */
- public void setColourText(boolean state)
- {
- showColourText = state;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param state
- * DOCUMENT ME!
- */
- public void setShowBoxes(boolean state)
- {
- showBoxes = state;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getWrapAlignment()
- {
- return wrapAlignment;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getShowText()
- {
- return showText;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getShowBoxes()
- {
- return showBoxes;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public char getGapCharacter()
- {
- return getAlignment().getGapCharacter();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param gap
- * DOCUMENT ME!
- */
- public void setGapCharacter(char gap)
- {
- if (getAlignment() != null)
- {
- getAlignment().setGapCharacter(gap);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param thresh
- * DOCUMENT ME!
- */
- public void setThreshold(int thresh)
- {
- threshold = thresh;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getThreshold()
- {
- return threshold;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param inc
- * DOCUMENT ME!
- */
- public void setIncrement(int inc)
- {
- increment = inc;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getIncrement()
- {
- return increment;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public ColumnSelection getColumnSelection()
- {
- return colSel;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param tree
- * DOCUMENT ME!
- */
- public void setCurrentTree(NJTree tree)
- {
- currentTree = tree;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public NJTree getCurrentTree()
- {
- return currentTree;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param b
- * DOCUMENT ME!
- */
- public void setColourAppliesToAllGroups(boolean b)
- {
- colourAppliesToAllGroups = b;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getColourAppliesToAllGroups()
- {
- return colourAppliesToAllGroups;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getShowJVSuffix()
- {
- return showJVSuffix;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param b
- * DOCUMENT ME!
- */
- public void setShowJVSuffix(boolean b)
- {
- showJVSuffix = b;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getShowAnnotation()
- {
- return showAnnotation;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param b
- * DOCUMENT ME!
- */
- public void setShowAnnotation(boolean b)
- {
- showAnnotation = b;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getScaleAboveWrapped()
- {
- return scaleAboveWrapped;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getScaleLeftWrapped()
- {
- return scaleLeftWrapped;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getScaleRightWrapped()
- {
- return scaleRightWrapped;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param b
- * DOCUMENT ME!
- */
- public void setScaleAboveWrapped(boolean b)
- {
- scaleAboveWrapped = b;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param b
- * DOCUMENT ME!
- */
- public void setScaleLeftWrapped(boolean b)
- {
- scaleLeftWrapped = b;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param b
- * DOCUMENT ME!
- */
- public void setScaleRightWrapped(boolean b)
- {
- scaleRightWrapped = b;
- }
-
- /**
- * Property change listener for changes in alignment
- *
- * @param listener
- * DOCUMENT ME!
- */
- public void addPropertyChangeListener(
- java.beans.PropertyChangeListener listener)
- {
- changeSupport.addPropertyChangeListener(listener);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param listener
- * DOCUMENT ME!
- */
- public void removePropertyChangeListener(
- java.beans.PropertyChangeListener listener)
- {
- changeSupport.removePropertyChangeListener(listener);
- }
-
- /**
- * Property change listener for changes in alignment
- *
- * @param prop
- * DOCUMENT ME!
- * @param oldvalue
- * DOCUMENT ME!
- * @param newvalue
- * DOCUMENT ME!
- */
- public void firePropertyChange(String prop, Object oldvalue,
- Object newvalue)
- {
- changeSupport.firePropertyChange(prop, oldvalue, newvalue);
- }
-
- public void setIgnoreGapsConsensus(boolean b, AlignmentPanel ap)
- {
- ignoreGapsInConsensusCalculation = b;
- updateConsensus(ap);
- if (globalColourScheme != null)
- {
- globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
- ignoreGapsInConsensusCalculation);
- }
- }
-
- public boolean getIgnoreGapsConsensus()
- {
- return ignoreGapsInConsensusCalculation;
- }
-
- public void setDataset(boolean b)
- {
- isDataset = b;
- }
-
- public boolean isDataset()
- {
- return isDataset;
- }
-
- public void hideSelectedColumns()
- {
- if (colSel.size() < 1)
- {
- return;
- }
-
- colSel.hideSelectedColumns();
- setSelectionGroup(null);
-
- hasHiddenColumns = true;
- }
-
- public void hideColumns(int start, int end)
- {
- if (start == end)
- {
- colSel.hideColumns(start);
- }
- else
- {
- colSel.hideColumns(start, end);
- }
-
- hasHiddenColumns = true;
- }
-
- public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
- {
- int sSize = sg.getSize();
- if (sSize < 2)
- {
- return;
- }
-
- if (hiddenRepSequences == null)
- {
- hiddenRepSequences = new Hashtable();
- }
-
- hiddenRepSequences.put(repSequence, sg);
-
- // Hide all sequences except the repSequence
- SequenceI[] seqs = new SequenceI[sSize - 1];
- int index = 0;
- for (int i = 0; i < sSize; i++)
- {
- if (sg.getSequenceAt(i) != repSequence)
- {
- if (index == sSize - 1)
- {
- return;
- }
-
- seqs[index++] = sg.getSequenceAt(i);
- }
- }
- sg.setSeqrep(repSequence);
- sg.setHidereps(true);
- hideSequence(seqs);
-
- }
-
- public void hideAllSelectedSeqs()
- {
- if (selectionGroup == null || selectionGroup.getSize() < 1)
- {
- return;
- }
-
- SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
-
- hideSequence(seqs);
-
- setSelectionGroup(null);
- }
-
- public void hideSequence(SequenceI[] seq)
- {
- if (seq != null)
- {
- for (int i = 0; i < seq.length; i++)
- {
- alignment.getHiddenSequences().hideSequence(seq[i]);
- }
- hasHiddenRows = true;
- firePropertyChange("alignment", null, alignment.getSequences());
- }
- }
-
- public void showSequence(int index)
- {
- Vector tmp = alignment.getHiddenSequences().showSequence(index,
- hiddenRepSequences);
- if (tmp.size() > 0)
- {
- if (selectionGroup == null)
- {
- selectionGroup = new SequenceGroup();
- selectionGroup.setEndRes(alignment.getWidth() - 1);
- }
-
- for (int t = 0; t < tmp.size(); t++)
- {
- selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
- }
- firePropertyChange("alignment", null, alignment.getSequences());
- sendSelection();
- }
-
- if (alignment.getHiddenSequences().getSize() < 1)
- {
- hasHiddenRows = false;
- }
- }
-
- public void showColumn(int col)
- {
- colSel.revealHiddenColumns(col);
- if (colSel.getHiddenColumns() == null)
- {
- hasHiddenColumns = false;
- }
- }
-
- public void showAllHiddenColumns()
- {
- colSel.revealAllHiddenColumns();
- hasHiddenColumns = false;
- }
-
- public void showAllHiddenSeqs()
- {
- if (alignment.getHiddenSequences().getSize() > 0)
- {
- if (selectionGroup == null)
- {
- selectionGroup = new SequenceGroup();
- selectionGroup.setEndRes(alignment.getWidth() - 1);
- }
- Vector tmp = alignment.getHiddenSequences().showAll(
- hiddenRepSequences);
- for (int t = 0; t < tmp.size(); t++)
- {
- selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
- }
- firePropertyChange("alignment", null, alignment.getSequences());
- sendSelection();
- hasHiddenRows = false;
- hiddenRepSequences = null;
- }
- }
-
- public void invertColumnSelection()
- {
- colSel.invertColumnSelection(0, alignment.getWidth());
- }
-
- public int adjustForHiddenSeqs(int alignmentIndex)
- {
- return alignment.getHiddenSequences().adjustForHiddenSeqs(
- alignmentIndex);
- }
-
- /**
- * This method returns an array of new SequenceI objects derived from the
- * whole alignment or just the current selection with start and end points
- * adjusted
- *
- * @note if you need references to the actual SequenceI objects in the
- * alignment or currently selected then use getSequenceSelection()
- * @return selection as new sequenceI objects
- */
- public SequenceI[] getSelectionAsNewSequence()
- {
- SequenceI[] sequences;
-
- if (selectionGroup == null)
- {
- sequences = alignment.getSequencesArray();
- AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
- for (int i = 0; i < sequences.length; i++)
- {
- sequences[i] = new Sequence(sequences[i], annots); // construct new
- // sequence with
- // subset of visible
- // annotation
- }
- }
- else
- {
- sequences = selectionGroup.getSelectionAsNewSequences(alignment);
- }
-
- return sequences;
- }
-
- /**
- * get the currently selected sequence objects or all the sequences in the
- * alignment.
- *
- * @return array of references to sequence objects
- */
- public SequenceI[] getSequenceSelection()
- {
- SequenceI[] sequences = null;
- if (selectionGroup != null)
- {
- sequences = selectionGroup.getSequencesInOrder(alignment);
- }
- if (sequences == null)
+ if (getAlignment() != null)
{
- sequences = alignment.getSequencesArray();
+ getAlignment().setGapCharacter(gap);
}
- return sequences;
- }
-
- /**
- * This method returns the visible alignment as text, as seen on the GUI, ie
- * if columns are hidden they will not be returned in the result. Use this for
- * calculating trees, PCA, redundancy etc on views which contain hidden
- * columns.
- *
- * @return String[]
- */
- public jalview.datamodel.CigarArray getViewAsCigars(
- boolean selectedRegionOnly)
- {
- return new jalview.datamodel.CigarArray(alignment, (hasHiddenColumns ? colSel : null), (selectedRegionOnly ? selectionGroup : null));
}
/**
- * return a compact representation of the current alignment selection to pass
- * to an analysis function
- *
- * @param selectedOnly
- * boolean true to just return the selected view
- * @return AlignmentView
- */
- public jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly)
- {
- return getAlignmentView(selectedOnly, false);
- }
-
- /**
- * return a compact representation of the current alignment selection to pass
- * to an analysis function
+ * DOCUMENT ME!
*
- * @param selectedOnly
- * boolean true to just return the selected view
- * @param markGroups
- * boolean true to annotate the alignment view with groups on the alignment (and intersecting with selected region if selectedOnly is true)
- * @return AlignmentView
+ * @return DOCUMENT ME!
*/
- public jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups)
+ public ColumnSelection getColumnSelection()
{
- return new AlignmentView(alignment, colSel, selectionGroup, hasHiddenColumns, selectedOnly, markGroups);
+ return colSel;
}
/**
- * This method returns the visible alignment as text, as seen on the GUI, ie
- * if columns are hidden they will not be returned in the result. Use this for
- * calculating trees, PCA, redundancy etc on views which contain hidden
- * columns.
+ * DOCUMENT ME!
*
- * @return String[]
+ * @param tree
+ * DOCUMENT ME!
*/
- public String[] getViewAsString(boolean selectedRegionOnly)
- {
- String[] selection = null;
- SequenceI[] seqs = null;
- int i, iSize;
- int start = 0, end = 0;
- if (selectedRegionOnly && selectionGroup != null)
- {
- iSize = selectionGroup.getSize();
- seqs = selectionGroup.getSequencesInOrder(alignment);
- start = selectionGroup.getStartRes();
- end = selectionGroup.getEndRes() + 1;
- }
- else
- {
- iSize = alignment.getHeight();
- seqs = alignment.getSequencesArray();
- end = alignment.getWidth();
- }
-
- selection = new String[iSize];
- if (hasHiddenColumns)
- {
- selection = colSel.getVisibleSequenceStrings(start, end, seqs);
- }
- else
- {
- for (i = 0; i < iSize; i++)
- {
- selection[i] = seqs[i].getSequenceAsString(start, end);
- }
-
- }
- return selection;
- }
-
- public int[][] getVisibleRegionBoundaries(int min, int max)
- {
- Vector regions = new Vector();
- int start = min;
- int end = max;
-
- do
- {
- if (hasHiddenColumns)
- {
- if (start == 0)
- {
- start = colSel.adjustForHiddenColumns(start);
- }
-
- end = colSel.getHiddenBoundaryRight(start);
- if (start == end)
- {
- end = max;
- }
- if (end > max)
- {
- end = max;
- }
- }
-
- regions.addElement(new int[]
- { start, end });
-
- if (hasHiddenColumns)
- {
- start = colSel.adjustForHiddenColumns(end);
- start = colSel.getHiddenBoundaryLeft(start) + 1;
- }
- } while (end < max);
-
- int[][] startEnd = new int[regions.size()][2];
-
- regions.copyInto(startEnd);
-
- return startEnd;
-
- }
-
- public boolean getShowHiddenMarkers()
- {
- return showHiddenMarkers;
- }
-
- public void setShowHiddenMarkers(boolean show)
- {
- showHiddenMarkers = show;
- }
-
- public String getSequenceSetId()
+ public void setCurrentTree(NJTree tree)
{
- if (sequenceSetID == null)
- {
- sequenceSetID = alignment.hashCode() + "";
- }
-
- return sequenceSetID;
+ currentTree = tree;
}
/**
- * unique viewId for synchronizing state with stored Jalview Project
+ * DOCUMENT ME!
*
+ * @return DOCUMENT ME!
*/
- private String viewId = null;
-
- public String getViewId()
- {
- if (viewId == null)
- {
- viewId = this.getSequenceSetId() + "." + this.hashCode() + "";
- }
- return viewId;
- }
-
- public void alignmentChanged(AlignmentPanel ap)
- {
- if (padGaps)
- {
- alignment.padGaps();
- }
- if (hconsensus != null && autoCalculateConsensus)
- {
- updateConservation(ap);
- }
- if (autoCalculateConsensus)
- {
- updateConsensus(ap);
- }
-
- // Reset endRes of groups if beyond alignment width
- int alWidth = alignment.getWidth();
- Vector groups = alignment.getGroups();
- if (groups != null)
- {
- for (int i = 0; i < groups.size(); i++)
- {
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
- if (sg.getEndRes() > alWidth)
- {
- sg.setEndRes(alWidth - 1);
- }
- }
- }
-
- if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)
- {
- selectionGroup.setEndRes(alWidth - 1);
- }
-
- resetAllColourSchemes();
-
- // alignment.adjustSequenceAnnotations();
- }
-
- void resetAllColourSchemes()
- {
- ColourSchemeI cs = globalColourScheme;
- if (cs != null)
- {
- if (cs instanceof ClustalxColourScheme)
- {
- ((ClustalxColourScheme) cs).resetClustalX(alignment.getSequences(),
- alignment.getWidth());
- }
-
- cs.setConsensus(hconsensus);
- if (cs.conservationApplied())
- {
- Alignment al = (Alignment) alignment;
- Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3, al.getSequences(), 0,
- al.getWidth() - 1);
- c.calculate();
- c.verdict(false, ConsPercGaps);
-
- cs.setConservation(c);
- }
- }
-
- int s, sSize = alignment.getGroups().size();
- for (s = 0; s < sSize; s++)
- {
- SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s);
- if (sg.cs != null && sg.cs instanceof ClustalxColourScheme)
- {
- ((ClustalxColourScheme) sg.cs).resetClustalX(
- sg.getSequences(hiddenRepSequences), sg.getWidth());
- }
- sg.recalcConservation();
- }
- }
-
- 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)
+ public NJTree getCurrentTree()
{
- if (sequenceColours == null)
- {
- sequenceColours = new Hashtable();
- }
-
- if (col == null)
- {
- sequenceColours.remove(seq);
- }
- else
- {
- sequenceColours.put(seq, col);
- }
+ return currentTree;
}
/**
@@ -1847,139 +602,55 @@ public class AlignViewport implements SelectionSource, VamsasSource
end = alignment.getWidth();
}
viscontigs = colSel.getVisibleContigs(start, end);
- return viscontigs;
- }
-
- /**
- * get hash of undo and redo list for the alignment
- *
- * @return long[] { historyList.hashCode, redoList.hashCode };
- */
- public long[] getUndoRedoHash()
- {
- if (historyList == null || redoList == null)
- return new long[]
- { -1, -1 };
- return new long[]
- { historyList.hashCode(), this.redoList.hashCode() };
- }
-
- /**
- * test if a particular set of hashcodes are different to the hashcodes for
- * the undo and redo list.
- *
- * @param undoredo
- * the stored set of hashcodes as returned by getUndoRedoHash
- * @return true if the hashcodes differ (ie the alignment has been edited) or
- * the stored hashcode array differs in size
- */
- public boolean isUndoRedoHashModified(long[] undoredo)
- {
- if (undoredo == null)
- {
- return true;
- }
- long[] cstate = getUndoRedoHash();
- if (cstate.length != undoredo.length)
- {
- return true;
- }
-
- for (int i = 0; i < cstate.length; i++)
- {
- if (cstate[i] != undoredo[i])
- {
- return true;
- }
- }
- return false;
- }
-
- public boolean getCentreColumnLabels()
- {
- return centreColumnLabels;
- }
-
- public void setCentreColumnLabels(boolean centrecolumnlabels)
- {
- centreColumnLabels = centrecolumnlabels;
- }
-
- public void updateSequenceIdColours()
- {
- Vector groups = alignment.getGroups();
- if (sequenceColours == null)
- {
- sequenceColours = new Hashtable();
- }
- for (int ig = 0, igSize = groups.size(); ig < igSize; ig++)
- {
- SequenceGroup sg = (SequenceGroup) groups.elementAt(ig);
- if (sg.idColour != null)
- {
- Vector sqs = sg.getSequences(hiddenRepSequences);
- for (int s = 0, sSize = sqs.size(); s < sSize; s++)
- {
- sequenceColours.put(sqs.elementAt(s), sg.idColour);
- }
- }
- }
- }
-
- /**
- * enable or disable the display of Database Cross References in the sequence
- * ID tooltip
- */
- public void setShowDbRefs(boolean show)
- {
- showdbrefs = show;
- }
-
- /**
- *
- * @return true if Database References are to be displayed on tooltips.
- */
- public boolean isShowDbRefs()
- {
- return showdbrefs;
- }
-
- /**
- *
- * @return true if Non-positional features are to be displayed on tooltips.
- */
- public boolean isShowNpFeats()
- {
- return shownpfeats;
- }
-
- /**
- * enable or disable the display of Non-Positional sequence features in the
- * sequence ID tooltip
- *
- * @param show
- */
- public void setShowNpFeats(boolean show)
- {
- shownpfeats = show;
+ return viscontigs;
}
/**
+ * get hash of undo and redo list for the alignment
*
- * @return true if view has hidden rows
+ * @return long[] { historyList.hashCode, redoList.hashCode };
*/
- public boolean hasHiddenRows()
+ public long[] getUndoRedoHash()
{
- return hasHiddenRows;
+ // TODO: JAL-1126
+ if (historyList == null || redoList == null)
+ {
+ return new long[]
+ { -1, -1 };
+ }
+ return new long[]
+ { historyList.hashCode(), this.redoList.hashCode() };
}
/**
+ * test if a particular set of hashcodes are different to the hashcodes for
+ * the undo and redo list.
*
- * @return true if view has hidden columns
+ * @param undoredo
+ * the stored set of hashcodes as returned by getUndoRedoHash
+ * @return true if the hashcodes differ (ie the alignment has been edited) or
+ * the stored hashcode array differs in size
*/
- public boolean hasHiddenColumns()
+ public boolean isUndoRedoHashModified(long[] undoredo)
{
- return hasHiddenColumns;
+ if (undoredo == null)
+ {
+ return true;
+ }
+ long[] cstate = getUndoRedoHash();
+ if (cstate.length != undoredo.length)
+ {
+ return true;
+ }
+
+ for (int i = 0; i < cstate.length; i++)
+ {
+ if (cstate[i] != undoredo[i])
+ {
+ return true;
+ }
+ }
+ return false;
}
/**
@@ -2008,46 +679,9 @@ public class AlignViewport implements SelectionSource, VamsasSource
return followSelection;
}
- private long sgrouphash = -1, colselhash = -1;
-
- boolean showSeqFeaturesHeight;
-
- /**
- * checks current SelectionGroup against record of last hash value, and
- * updates record.
- * @param b update the record of last hash value
- *
- * @return true if SelectionGroup changed since last call (when b is true)
- */
- boolean isSelectionGroupChanged(boolean b)
- {
- int hc = (selectionGroup == null || selectionGroup.getSize()==0) ? -1 : selectionGroup.hashCode();
- if (hc!=-1 && hc != sgrouphash)
- {
- if (b) {sgrouphash = hc;}
- return true;
- }
- return false;
- }
-
/**
- * checks current colsel against record of last hash value, and optionally updates
- * record.
-
- * @param b update the record of last hash value
- * @return true if colsel changed since last call (when b is true)
+ * Send the current selection to be broadcast to any selection listeners.
*/
- boolean isColSelChanged(boolean b)
- {
- int hc = (colSel == null || colSel.size()==0) ? -1 : colSel.hashCode();
- if (hc!=-1 && hc != colselhash)
- {
- if (b) {colselhash = hc;}
- return true;
- }
- return false;
- }
-
public void sendSelection()
{
jalview.structure.StructureSelectionManager
@@ -2056,28 +690,6 @@ public class AlignViewport implements SelectionSource, VamsasSource
new ColumnSelection(getColumnSelection()), this);
}
- public void setShowSequenceFeaturesHeight(boolean selected)
- {
- showSeqFeaturesHeight = selected;
- }
-
- public boolean getShowSequenceFeaturesHeight()
- {
- return showSeqFeaturesHeight;
- }
-
- boolean showUnconserved = false;
-
- public boolean getShowUnconserved()
- {
- return showUnconserved;
- }
-
- public void setShowUnconserved(boolean showunconserved)
- {
- showUnconserved = showunconserved;
- }
-
/**
* return the alignPanel containing the given viewport. Use this to get the
* components currently handling the given viewport.
@@ -2090,7 +702,6 @@ public class AlignViewport implements SelectionSource, VamsasSource
{
AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this
.getSequenceSetId());
- AlignmentPanel ap = null;
for (int p = 0; aps != null && p < aps.length; p++)
{
if (aps[p].av == this)
@@ -2112,174 +723,445 @@ public class AlignViewport implements SelectionSource, VamsasSource
}
/**
- * should conservation rows be shown for groups
- */
- boolean showGroupConservation = false;
-
- /**
- * should consensus rows be shown for groups
- */
- boolean showGroupConsensus = false;
-
- /**
- * should consensus profile be rendered by default
- */
- public boolean showSequenceLogo = false;
-
- /**
- * should consensus histograms be rendered by default
+ * synthesize a column selection if none exists so it covers the given
+ * selection group. if wholewidth is false, no column selection is made if the
+ * selection group covers the whole alignment width.
+ *
+ * @param sg
+ * @param wholewidth
*/
- public boolean showConsensusHistogram = true;
+ public void expandColSelection(SequenceGroup sg, boolean wholewidth)
+ {
+ int sgs, sge;
+ if (sg != null
+ && (sgs = sg.getStartRes()) >= 0
+ && sg.getStartRes() <= (sge = sg.getEndRes())
+ && (colSel == null || colSel.getSelected() == null || colSel
+ .getSelected().size() == 0))
+ {
+ if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
+ {
+ // do nothing
+ return;
+ }
+ if (colSel == null)
+ {
+ colSel = new ColumnSelection();
+ }
+ for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
+ {
+ colSel.addElement(cspos);
+ }
+ }
+ }
/**
- * @return the showConsensusProfile
+ * Returns the (Desktop) instance of the StructureSelectionManager
*/
- public boolean isShowSequenceLogo()
+ @Override
+ public StructureSelectionManager getStructureSelectionManager()
{
- return showSequenceLogo;
+ return StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
}
/**
- * @param showSequenceLogo
- * the new value
+ *
+ * @param pdbEntries
+ * @return a series of SequenceI arrays, one for each PDBEntry, listing which
+ * sequence in the alignment holds a reference to it
*/
- public void setShowSequenceLogo(boolean showSequenceLogo)
+ public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
{
- if (showSequenceLogo != this.showSequenceLogo)
+ ArrayList seqvectors = new ArrayList();
+ for (PDBEntry pdb : pdbEntries)
{
- // TODO: decouple settings setting from calculation when refactoring
- // annotation update method from alignframe to viewport
- this.showSequenceLogo = showSequenceLogo;
- if (consensusThread != null)
+ ArrayList seqs = new ArrayList();
+ for (int i = 0; i < alignment.getHeight(); i++)
{
- consensusThread.updateAnnotation();
+ Vector pdbs = alignment.getSequenceAt(i).getDatasetSequence()
+ .getPDBId();
+ if (pdbs == null)
+ {
+ continue;
+ }
+ SequenceI sq;
+ for (int p = 0; p < pdbs.size(); p++)
+ {
+ PDBEntry p1 = (PDBEntry) pdbs.elementAt(p);
+ if (p1.getId().equals(pdb.getId()))
+ {
+ if (!seqs.contains(sq = alignment.getSequenceAt(i)))
+ {
+ seqs.add(sq);
+ }
+
+ continue;
+ }
+ }
}
+ seqvectors.add(seqs.toArray(new SequenceI[seqs.size()]));
}
- this.showSequenceLogo = showSequenceLogo;
+ return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
}
- /**
- * @param showConsensusHistogram
- * the showConsensusHistogram to set
- */
- public void setShowConsensusHistogram(boolean showConsensusHistogram)
+ public boolean isNormaliseSequenceLogo()
{
- this.showConsensusHistogram = showConsensusHistogram;
+ return normaliseSequenceLogo;
}
- /**
- * @return the showGroupConservation
- */
- public boolean isShowGroupConservation()
+ public void setNormaliseSequenceLogo(boolean state)
{
- return showGroupConservation;
+ normaliseSequenceLogo = state;
}
/**
- * @param showGroupConservation
- * the showGroupConservation to set
+ *
+ * @return true if alignment characters should be displayed
*/
- public void setShowGroupConservation(boolean showGroupConservation)
+ public boolean isValidCharWidth()
{
- this.showGroupConservation = showGroupConservation;
+ return validCharWidth;
}
- /**
- * @return the showGroupConsensus
- */
- public boolean isShowGroupConsensus()
+ private Hashtable calcIdParams = new Hashtable();
+
+ private boolean showAutocalculatedAbove;
+
+ public AutoCalcSetting getCalcIdSettingsFor(String calcId)
{
- return showGroupConsensus;
+ return calcIdParams.get(calcId);
}
- /**
- * @param showGroupConsensus
- * the showGroupConsensus to set
- */
- public void setShowGroupConsensus(boolean showGroupConsensus)
+ public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings,
+ boolean needsUpdate)
+ {
+ calcIdParams.put(calcId, settings);
+ // TODO: create a restart list to trigger any calculations that need to be
+ // restarted after load
+ // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
+ if (needsUpdate)
+ {
+ Cache.log.debug("trigger update for " + calcId);
+ }
+ }
+
+ protected SequenceAnnotationOrder getSortAnnotationsBy()
+ {
+ return sortAnnotationsBy;
+ }
+
+ protected void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy)
+ {
+ this.sortAnnotationsBy = sortAnnotationsBy;
+ }
+
+ protected boolean isShowAutocalculatedAbove()
{
- this.showGroupConsensus = showGroupConsensus;
+ return showAutocalculatedAbove;
+ }
+
+ protected void setShowAutocalculatedAbove(boolean showAutocalculatedAbove)
+ {
+ this.showAutocalculatedAbove = showAutocalculatedAbove;
}
/**
+ * Method called when another alignment's edit (or possibly other) command is
+ * broadcast to here.
+ *
+ * To allow for sequence mappings (e.g. protein to cDNA), we have to first
+ * 'unwind' the command on the source sequences (in simulation, not in fact),
+ * and then for each edit in turn:
+ *
+ * - compute the equivalent edit on the mapped sequences
+ * - apply the mapped edit
+ * - 'apply' the source edit to the working copy of the source sequences
+ *
*
- * @return flag to indicate if the consensus histogram should be rendered by
- * default
+ * @param command
+ * @param undo
+ * @param ssm
*/
- public boolean isShowConsensusHistogram()
+ @Override
+ public void mirrorCommand(CommandI command, boolean undo,
+ StructureSelectionManager ssm, VamsasSource source)
{
- return this.showConsensusHistogram;
+ /*
+ * Do nothing unless we are a 'complement' of the source. May replace this
+ * with direct calls not via SSM.
+ */
+ if (source instanceof AlignViewportI
+ && ((AlignViewportI) source).getCodingComplement() == this)
+ {
+ // ok to continue;
+ }
+ else
+ {
+ return;
+ }
+
+ CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(),
+ getGapCharacter());
+ if (mappedCommand != null)
+ {
+ AlignmentI[] views = getAlignPanel().alignFrame.getViewAlignments();
+ mappedCommand.doCommand(views);
+ getAlignPanel().alignmentChanged();
+ }
}
/**
- * synthesize a column selection if none exists so it covers the given
- * selection group. if wholewidth is false, no column selection is made if the
- * selection group covers the whole alignment width.
+ * Add the sequences from the given alignment to this viewport. Optionally,
+ * may give the user the option to open a new frame, or split panel, with cDNA
+ * and protein linked.
*
- * @param sg
- * @param wholewidth
+ * @param al
+ * @param title
*/
- public void expandColSelection(SequenceGroup sg, boolean wholewidth)
+ public void addAlignment(AlignmentI al, String title)
{
- int sgs, sge;
- if (sg != null
- && (sgs = sg.getStartRes()) >= 0
- && sg.getStartRes() <= (sge = sg.getEndRes())
- && (colSel == null || colSel.getSelected() == null || colSel
- .getSelected().size() == 0))
+ // TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different
+
+ // JBPComment: title is a largely redundant parameter at the moment
+ // JBPComment: this really should be an 'insert/pre/append' controller
+ // JBPComment: but the DNA/Protein check makes it a bit more complex
+
+ // refactored from FileLoader / CutAndPasteTransfer / SequenceFetcher with
+ // this comment:
+ // TODO: create undo object for this JAL-1101
+
+ /*
+ * If one alignment is protein and one nucleotide, with at least one
+ * sequence name in common, offer to open a linked alignment.
+ */
+ if (getAlignment().isNucleotide() != al.isNucleotide())
{
- if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
- {
- // do nothing
- return;
- }
- if (colSel == null)
- {
- colSel = new ColumnSelection();
- }
- for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
+ // TODO: JAL-845 try a bit harder to link up imported sequences
+ final Set sequenceNames = getAlignment().getSequenceNames();
+ sequenceNames.retainAll(al.getSequenceNames());
+ if (!sequenceNames.isEmpty()) // at least one sequence name in both
{
- colSel.addElement(cspos);
+ if (openLinkedAlignment(al, title))
+ {
+ return;
+ }
}
}
- }
+ // TODO: JAL-407 regardless of above - identical sequences (based on ID and
+ // provenance) should share the same dataset sequence
- public StructureSelectionManager getStructureSelectionManager()
- {
- return StructureSelectionManager.getStructureSelectionManager(Desktop.instance);
+ for (int i = 0; i < al.getHeight(); i++)
+ {
+ getAlignment().addSequence(al.getSequenceAt(i));
+ }
+ // TODO this call was done by SequenceFetcher but not FileLoader or
+ // CutAndPasteTransfer. Is it needed?
+ // JBPComment: this repositions the view to show the new sequences
+ // JBPComment: so it is needed for UX
+ setEndSeq(getAlignment().getHeight());
+ firePropertyChange("alignment", null, getAlignment().getSequences());
}
/**
+ * Show a dialog with the option to open and link (cDNA <-> protein) as a new
+ * alignment. Returns true if the new alignment was opened, false if not,
+ * because the user declined the offer.
*
- * @param pdbEntries
- * @return a series of SequenceI arrays, one for each PDBEntry, listing which sequence in the alignment holds a reference to it
+ * @param title
*/
- public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
+ protected boolean openLinkedAlignment(AlignmentI al, String title)
{
- ArrayList seqvectors = new ArrayList();
- for (PDBEntry pdb: pdbEntries) {
- ArrayList seqs = new ArrayList();
- for (int i = 0; i < alignment.getHeight(); i++)
+ String[] options = new String[]
+ { MessageManager.getString("action.no"),
+ MessageManager.getString("label.split_window"),
+ MessageManager.getString("label.new_window"), };
+ final String question = JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.open_linked_alignment?"));
+ int response = JOptionPane.showOptionDialog(Desktop.desktop, question,
+ MessageManager.getString("label.open_linked_alignment"),
+ JOptionPane.DEFAULT_OPTION, JOptionPane.PLAIN_MESSAGE, null,
+ options, options[0]);
+
+ if (response != 1 && response != 2)
{
- Vector pdbs = alignment.getSequenceAt(i)
- .getDatasetSequence().getPDBId();
- if (pdbs == null)
- continue;
- SequenceI sq;
- for (int p = 0; p < pdbs.size(); p++)
- {
- PDBEntry p1 = (PDBEntry) pdbs.elementAt(p);
- if (p1.getId().equals(pdb.getId()))
- {
- if (!seqs.contains(sq=alignment.getSequenceAt(i)))
- seqs.add(sq);
+ return false;
+ }
+ final boolean openSplitPane = (response == 1);
+ final boolean openInNewWindow = (response == 2);
- continue;
- }
- }
+ /*
+ * Create the AlignFrame first (which creates the new alignment's datasets),
+ * before attempting sequence mapping.
+ */
+ AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ newAlignFrame.setTitle(title);
+
+ /*
+ * Identify protein and dna alignments. Make a copy of this one if opening
+ * in a new split pane.
+ */
+ AlignmentI thisAlignment = openSplitPane ? new Alignment(getAlignment())
+ : getAlignment();
+ AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
+ final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
+
+ newAlignFrame.statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_loaded_file", new Object[]
+ { title }));
+
+ // TODO if we want this (e.g. to enable reload of the alignment from file),
+ // we will need to add parameters to the stack.
+ // if (!protocol.equals(AppletFormatAdapter.PASTE))
+ // {
+ // alignFrame.setFileName(file, format);
+ // }
+
+ if (openInNewWindow)
+ {
+ Desktop.addInternalFrame(newAlignFrame, title,
+ AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
}
- seqvectors.add(seqs.toArray(new SequenceI[seqs.size()]));
+
+ /*
+ * Try to find mappings for at least one sequence. Any mappings made will be
+ * added to the protein alignment.
+ */
+ MappingResult mapped = AlignmentUtils.mapProteinToCdna(protein, cdna);
+ if (mapped != MappingResult.Mapped)
+ {
+ /*
+ * No mapping possible - warn the user, but leave window open.
+ */
+ final String msg = JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.mapping_failed"));
+ JOptionPane.showInternalMessageDialog(Desktop.desktop, msg,
+ MessageManager.getString("label.no_mappings"),
+ JOptionPane.WARNING_MESSAGE);
}
- return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
+
+ try
+ {
+ newAlignFrame.setMaximum(jalview.bin.Cache.getDefault(
+ "SHOW_FULLSCREEN",
+ false));
+ } catch (java.beans.PropertyVetoException ex)
+ {
+ }
+
+ if (openSplitPane)
+ {
+ protein = openSplitFrame(newAlignFrame, thisAlignment);
+ }
+
+ /*
+ * Register the mappings (held on the protein alignment) with the
+ * StructureSelectionManager (for mouseover linking).
+ */
+ final StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ ssm.addMappings(protein.getCodonFrames());
+
+ return true;
+ }
+
+ /**
+ * Helper method to open a new SplitFrame holding linked dna and protein
+ * alignments.
+ *
+ * @param newAlignFrame
+ * containing a new alignment to be shown
+ * @param existingAlignment
+ * an existing alignment to be copied for display in the split frame
+ * @return the protein alignment in the split frame
+ */
+ protected AlignmentI openSplitFrame(AlignFrame newAlignFrame,
+ AlignmentI existingAlignment)
+ {
+ // TODO: move this to a factory/controller method ?
+ /*
+ * Open in split pane. DNA sequence above, protein below.
+ */
+ AlignFrame copyMe = new AlignFrame(existingAlignment,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ copyMe.setTitle(getAlignPanel().alignFrame.getTitle());
+
+ AlignmentI al = newAlignFrame.viewport.getAlignment();
+ final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
+ : newAlignFrame;
+ final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame
+ : copyMe;
+ AlignmentI protein = proteinFrame.viewport.getAlignment();
+
+ cdnaFrame.setVisible(true);
+ proteinFrame.setVisible(true);
+ String linkedTitle = MessageManager
+ .getString("label.linked_view_title");
+ JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
+ Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
+
+ /*
+ * Set the frames to listen for each other's edit and sort commands.
+ */
+ final StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ ssm.addCommandListener(cdnaFrame.getViewport());
+ ssm.addCommandListener(proteinFrame.getViewport());
+
+ /*
+ * 'Coding complement' (dna/protein) views will mirror each others' edits,
+ * selections, sorting etc as decided from time to time by the relevant
+ * authorities.
+ */
+ proteinFrame.getViewport().setCodingComplement(cdnaFrame.getViewport());
+ return protein;
+ }
+
+ public AnnotationColumnChooser getAnnotationColumnSelectionState()
+ {
+ return annotationColumnSelectionState;
+ }
+
+ public void setAnnotationColumnSelectionState(
+ AnnotationColumnChooser currentAnnotationColumnSelectionState)
+ {
+ this.annotationColumnSelectionState = currentAnnotationColumnSelectionState;
+ }
+
+ @Override
+ public void setIdWidth(int i)
+ {
+ super.setIdWidth(i);
+ AlignmentPanel ap = getAlignPanel();
+ if (ap != null)
+ {
+ // modify GUI elements to reflect geometry change
+ Dimension idw = getAlignPanel().getIdPanel().getIdCanvas()
+ .getPreferredSize();
+ idw.width = i;
+ getAlignPanel().getIdPanel().getIdCanvas().setPreferredSize(idw);
+ }
+ }
+
+ public Rectangle getExplodedGeometry()
+ {
+ return explodedGeometry;
+ }
+
+ public void setExplodedGeometry(Rectangle explodedPosition)
+ {
+ this.explodedGeometry = explodedPosition;
+ }
+
+ public boolean isGatherViewsHere()
+ {
+ return gatherViewsHere;
+ }
+
+ public void setGatherViewsHere(boolean gatherViewsHere)
+ {
+ this.gatherViewsHere = gatherViewsHere;
}
}