X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=60430ed9bf8304a4bb11bbf64efa385a8af2056e;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=fa458a6ef044899dde24b17588aaeee1e7246a6c;hpb=890bd0eac47a4b0f55bd062a359c16a43c3780a0;p=jalview.git
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
old mode 100755
new mode 100644
index fa458a6..60430ed
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,4 +1,24 @@
/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * 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.
+ *
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
@@ -18,111 +38,124 @@
*/
package jalview.gui;
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.analysis.NJTree;
+import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
+import jalview.commands.CommandI;
+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.SelectionSource;
+import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.ws.params.AutoCalcSetting;
+
+import java.awt.Color;
+import java.awt.Container;
+import java.awt.Font;
+import java.awt.Rectangle;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Stack;
+import java.util.Vector;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
- * @version $Revision$
+ * @version $Revision: 1.141 $
*/
-public class AlignViewport
+public class AlignViewport extends AlignmentViewport implements
+ SelectionSource, VamsasSource, AlignViewportI
{
int startRes;
+
int endRes;
+
int startSeq;
+
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;
+
+ SequenceAnnotationOrder sortAnnotationsBy = null;
+
int charHeight;
+
int charWidth;
+
boolean validCharWidth;
+
int wrappedWidth;
+
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;
- // The following vector holds the features which are
- // currently visible, in the correct order or rendering
+ /**
+ * 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;
- 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;
String viewName;
- String sequenceSetID;
-
boolean gatherViewsHere = false;
- Stack historyList = new Stack();
- Stack redoList = new Stack();
+ Stack historyList = new Stack();
- Hashtable sequenceColours;
+ Stack redoList = new Stack();
int thresholdTextColour = 0;
+
Color textColour = Color.black;
+
Color textColour2 = Color.white;
boolean rightAlignIds = false;
- Hashtable hiddenRepSequences;
-
/**
* Creates a new AlignViewport object.
- *
- * @param al DOCUMENT ME!
+ *
+ * @param al
+ * alignment to view
*/
public AlignViewport(AlignmentI al)
{
@@ -131,9 +164,42 @@ public class AlignViewport
}
/**
+ * Create a new AlignViewport object with a specific sequence set ID
+ *
+ * @param al
+ * @param seqsetid
+ * (may be null - but potential for ambiguous constructor exception)
+ */
+ public AlignViewport(AlignmentI al, String seqsetid)
+ {
+ this(al, seqsetid, null);
+ }
+
+ public AlignViewport(AlignmentI al, String seqsetid, String viewid)
+ {
+ sequenceSetID = seqsetid;
+ viewId = viewid;
+ // TODO remove these once 2.4.VAMSAS release finished
+ if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
+ {
+ Cache.log.debug("Setting viewport's sequence set id : "
+ + sequenceSetID);
+ }
+ if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
+ {
+ Cache.log.debug("Setting viewport's view id : " + viewId);
+ }
+ setAlignment(al);
+ init();
+ }
+
+ /**
* Create a new AlignViewport with hidden regions
- * @param al AlignmentI
- * @param hiddenColumns ColumnSelection
+ *
+ * @param al
+ * AlignmentI
+ * @param hiddenColumns
+ * ColumnSelection
*/
public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns)
{
@@ -141,10 +207,71 @@ public class AlignViewport
if (hiddenColumns != null)
{
this.colSel = hiddenColumns;
- if (hiddenColumns.getHiddenColumns() != null)
+ if (hiddenColumns.getHiddenColumns() != null
+ && hiddenColumns.getHiddenColumns().size() > 0)
+ {
+ hasHiddenColumns = true;
+ }
+ else
+ {
+ hasHiddenColumns = false;
+ }
+ }
+ init();
+ }
+
+ /**
+ * New viewport with hidden columns and an existing sequence set id
+ *
+ * @param al
+ * @param hiddenColumns
+ * @param seqsetid
+ * (may be null)
+ */
+ public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
+ String seqsetid)
+ {
+ this(al, hiddenColumns, seqsetid, null);
+ }
+
+ /**
+ * New viewport with hidden columns and an existing sequence set id and viewid
+ *
+ * @param al
+ * @param hiddenColumns
+ * @param seqsetid
+ * (may be null)
+ * @param viewid
+ * (may be null)
+ */
+ public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
+ String seqsetid, String viewid)
+ {
+ sequenceSetID = seqsetid;
+ viewId = viewid;
+ // TODO remove these once 2.4.VAMSAS release finished
+ if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
+ {
+ Cache.log.debug("Setting viewport's sequence set id : "
+ + sequenceSetID);
+ }
+ if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
+ {
+ Cache.log.debug("Setting viewport's view id : " + viewId);
+ }
+ setAlignment(al);
+ if (hiddenColumns != null)
+ {
+ this.colSel = hiddenColumns;
+ if (hiddenColumns.getHiddenColumns() != null
+ && hiddenColumns.getHiddenColumns().size() > 0)
{
hasHiddenColumns = true;
}
+ else
+ {
+ hasHiddenColumns = false;
+ }
}
init();
}
@@ -162,10 +289,12 @@ public class AlignViewport
showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
-
+ centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false);
autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
- padGaps = Cache.getDefault("PAD_GAPS", true);
+ setPadGaps(Cache.getDefault("PAD_GAPS", true));
+ shownpfeats = Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true);
+ showdbrefs = Cache.getDefault("SHOW_DBREFS_TOOLTIP", true);
String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
@@ -186,7 +315,8 @@ public class AlignViewport
setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
- alignment.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
+ alignment
+ .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
// We must set conservation and consensus before setting colour,
// as Blosum and Clustal require this to be done
@@ -194,57 +324,30 @@ public class AlignViewport
{
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);
- }
- }
-
- 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);
+ 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);
+ showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
}
-
+ initAutoAnnotation();
if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
{
globalColourScheme = ColourSchemeProperty.getColour(alignment,
- jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
+ jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
if (globalColourScheme instanceof UserColourScheme)
{
globalColourScheme = UserDefinedColours.loadDefaultColours();
- ( (UserColourScheme) globalColourScheme).setThreshold(0,
- getIgnoreGapsConsensus());
+ ((UserColourScheme) globalColourScheme).setThreshold(0,
+ getIgnoreGapsConsensus());
}
if (globalColourScheme != null)
@@ -253,13 +356,22 @@ public class AlignViewport
}
}
- wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
+ 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);
}
/**
- * DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
+ * set the flag
+ *
+ * @param b
+ * features are displayed if true
*/
public void setShowSequenceFeatures(boolean b)
{
@@ -271,319 +383,22 @@ public class AlignViewport
return showSequenceFeatures;
}
- class ConservationThread
- extends Thread
- {
- AlignmentPanel ap;
- public ConservationThread(AlignmentPanel ap)
- {
- this.ap = ap;
- }
-
- public void run()
- {
- try
- {
- updatingConservation = true;
-
- while (UPDATING_CONSERVATION)
- {
- try
- {
- if (ap != null)
- {
- ap.paintAlignment(true);
- }
- Thread.sleep(200);
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- UPDATING_CONSERVATION = true;
-
- int alWidth = alignment.getWidth();
- if (alWidth < 0)
- {
- return;
- }
-
- Conservation cons = new jalview.analysis.Conservation("All",
- jalview.schemes.ResidueProperties.propHash, 3,
- alignment.getSequences(), 0, alWidth - 1);
-
- cons.calculate();
- cons.verdict(false, ConsPercGaps);
-
- if (quality != null)
- {
- cons.findQuality();
- }
-
- char[] sequence = cons.getConsSequence().getSequence();
- float minR;
- float minG;
- float minB;
- float maxR;
- float maxG;
- float maxB;
- minR = 0.3f;
- minG = 0.0f;
- minB = 0f;
- maxR = 1.0f - minR;
- maxG = 0.9f - minG;
- maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
-
- float min = 0f;
- float max = 11f;
- float qmin = 0f;
- float qmax = 0f;
-
- char c;
-
- conservation.annotations = new Annotation[alWidth];
-
- if (quality != null)
- {
- quality.graphMax = cons.qualityRange[1].floatValue();
- quality.annotations = new Annotation[alWidth];
- qmin = cons.qualityRange[0].floatValue();
- qmax = cons.qualityRange[1].floatValue();
- }
-
- for (int i = 0; i < alWidth; i++)
- {
- float value = 0;
-
- c = sequence[i];
-
- if (Character.isDigit(c))
- {
- value = (int) (c - '0');
- }
- else if (c == '*')
- {
- value = 11;
- }
- else if (c == '+')
- {
- value = 10;
- }
-
- float vprop = value - min;
- vprop /= max;
- conservation.annotations[i] =
- new Annotation(String.valueOf(c),
- String.valueOf(value), ' ', value,
- new Color(minR + (maxR * vprop),
- minG + (maxG * vprop),
- minB + (maxB * vprop)));
-
- // Quality calc
- if (quality != null)
- {
- value = ( (Double) cons.quality.get(i)).floatValue();
- vprop = value - qmin;
- vprop /= qmax;
- quality.annotations[i] = new Annotation(" ", String.valueOf(value),
- ' ',
- value,
- new Color(minR + (maxR * vprop),
- minG + (maxG * vprop),
- minB + (maxB * vprop)));
- }
- }
- }
- catch (OutOfMemoryError error)
- {
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
-
- public void run()
- {
- javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Out of memory calculating conservation!!"
- +
- "\nSee help files for increasing Java Virtual Machine memory."
- , "Out of memory",
- javax.swing.JOptionPane.WARNING_MESSAGE);
- }
- });
-
- conservation = null;
- quality = null;
-
- System.out.println("Conservation calculation: " + error);
- System.gc();
-
- }
-
- UPDATING_CONSERVATION = false;
- updatingConservation = false;
-
- if (ap != null)
- {
- ap.paintAlignment(true);
- }
-
- }
- }
-
- ConservationThread conservationThread;
-
- ConsensusThread consensusThread;
-
- boolean consUpdateNeeded = false;
-
- static boolean UPDATING_CONSENSUS = false;
-
- static boolean UPDATING_CONSERVATION = false;
-
- boolean updatingConsensus = false;
-
- boolean updatingConservation = false;
-
- /**
- * DOCUMENT ME!
- */
- public void updateConservation(final AlignmentPanel ap)
- {
- if (alignment.isNucleotide() || conservation == null)
- {
- return;
- }
-
- conservationThread = new ConservationThread(ap);
- conservationThread.start();
- }
-
/**
- * DOCUMENT ME!
+ * centre columnar annotation labels in displayed alignment annotation TODO:
+ * add to jalviewXML and annotation display settings
*/
- public void updateConsensus(final AlignmentPanel ap)
- {
- 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(true);
- }
-
- Thread.sleep(200);
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- UPDATING_CONSENSUS = true;
-
- try
- {
- int aWidth = alignment.getWidth();
- if (aWidth < 0)
- {
- return;
- }
-
- consensus.annotations = null;
- consensus.annotations = new Annotation[aWidth];
-
- hconsensus = new Hashtable[aWidth];
- AAFrequency.calculate(alignment.getSequencesArray(),
- 0,
- alignment.getWidth(),
- hconsensus);
-
- for (int i = 0; i < aWidth; i++)
- {
- float value = 0;
- if (ignoreGapsInConsensusCalculation)
- {
- value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)).
- floatValue();
- }
- else
- {
- value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)).
- floatValue();
- }
-
- String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();
- String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";
-
- if (maxRes.length() > 1)
- {
- mouseOver = "[" + maxRes + "] ";
- maxRes = "+";
- }
-
- mouseOver += ( (int) value + "%");
- consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
- value);
- }
-
- if (globalColourScheme != null)
- {
- globalColourScheme.setConsensus(hconsensus);
- }
+ boolean centreColumnLabels = false;
- }
- catch (OutOfMemoryError error)
- {
- alignment.deleteAnnotation(consensus);
-
- consensus = null;
- hconsensus = null;
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- public void run()
- {
- javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Out of memory calculating consensus!!"
- +
- "\nSee help files for increasing Java Virtual Machine memory."
- , "Out of memory",
- javax.swing.JOptionPane.WARNING_MESSAGE);
- }
- });
+ private boolean showdbrefs;
- System.out.println("Consensus calculation: " + error);
- System.gc();
- }
- UPDATING_CONSENSUS = false;
- updatingConsensus = false;
+ private boolean shownpfeats;
- if (ap != null)
- {
- ap.paintAlignment(true);
- }
- }
- }
+ // --------END Structure Conservation
/**
- * get the consensus sequence as displayed under the PID consensus annotation row.
+ * get the consensus sequence as displayed under the PID consensus annotation
+ * row.
+ *
* @return consensus sequence as a new sequence object
*/
public SequenceI getConsensusSeq()
@@ -613,174 +428,98 @@ public class AlignViewport
}
SequenceI sq = new Sequence("Consensus", seqs.toString());
- sq.setDescription("Percentage Identity Consensus " +
- ( (ignoreGapsInConsensusCalculation) ? " without gaps" :
- ""));
+ sq.setDescription("Percentage Identity Consensus "
+ + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
return sq;
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
- public SequenceGroup getSelectionGroup()
+ public int getStartRes()
{
- return selectionGroup;
+ return startRes;
}
/**
* DOCUMENT ME!
- *
- * @param sg DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
*/
- public void setSelectionGroup(SequenceGroup sg)
+ public int getEndRes()
{
- selectionGroup = sg;
+ return endRes;
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
- public boolean getConservationSelected()
+ public int getStartSeq()
{
- return conservationColourSelected;
+ return startSeq;
}
/**
* DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
+ *
+ * @param res
+ * DOCUMENT ME!
*/
- public void setConservationSelected(boolean b)
+ public void setStartRes(int res)
{
- conservationColourSelected = b;
+ this.startRes = res;
}
/**
* DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ *
+ * @param seq
+ * DOCUMENT ME!
*/
- public boolean getAbovePIDThreshold()
+ public void setStartSeq(int seq)
{
- return abovePIDThreshold;
+ this.startSeq = seq;
}
/**
* DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
+ *
+ * @param res
+ * DOCUMENT ME!
*/
- public void setAbovePIDThreshold(boolean b)
+ public void setEndRes(int res)
{
- abovePIDThreshold = b;
+ if (res > (alignment.getWidth() - 1))
+ {
+ // log.System.out.println(" Corrected res from " + res + " to maximum " +
+ // (alignment.getWidth()-1));
+ res = alignment.getWidth() - 1;
+ }
+
+ if (res < 0)
+ {
+ res = 0;
+ }
+
+ this.endRes = res;
}
/**
* DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ *
+ * @param seq
+ * DOCUMENT ME!
*/
- public int getStartRes()
+ public void setEndSeq(int seq)
{
- return startRes;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getEndRes()
- {
- return endRes;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getStartSeq()
- {
- return startSeq;
- }
-
- /**
- * 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!
- */
- public void setStartRes(int res)
- {
- this.startRes = res;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param seq DOCUMENT ME!
- */
- public void setStartSeq(int seq)
- {
- this.startSeq = seq;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param res DOCUMENT ME!
- */
- public void setEndRes(int res)
- {
- if (res > (alignment.getWidth() - 1))
- {
- // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
- res = alignment.getWidth() - 1;
- }
-
- if (res < 0)
- {
- res = 0;
- }
-
- this.endRes = res;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param seq DOCUMENT ME!
- */
- public void setEndSeq(int seq)
- {
- if (seq > alignment.getHeight())
- {
- seq = alignment.getHeight();
- }
+ if (seq > alignment.getHeight())
+ {
+ seq = alignment.getHeight();
+ }
if (seq < 0)
{
@@ -792,7 +531,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getEndSeq()
@@ -802,8 +541,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param f DOCUMENT ME!
+ *
+ * @param f
+ * DOCUMENT ME!
*/
public void setFont(Font f)
{
@@ -819,7 +559,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public Font getFont()
@@ -829,8 +569,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param w DOCUMENT ME!
+ *
+ * @param w
+ * DOCUMENT ME!
*/
public void setCharWidth(int w)
{
@@ -839,7 +580,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getCharWidth()
@@ -849,8 +590,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param h DOCUMENT ME!
+ *
+ * @param h
+ * DOCUMENT ME!
*/
public void setCharHeight(int h)
{
@@ -859,7 +601,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getCharHeight()
@@ -869,8 +611,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param w DOCUMENT ME!
+ *
+ * @param w
+ * DOCUMENT ME!
*/
public void setWrappedWidth(int w)
{
@@ -879,7 +622,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getWrappedWidth()
@@ -889,7 +632,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public AlignmentI getAlignment()
@@ -899,18 +642,30 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param align 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 != null && alignment.getCodonFrames() != null)
+ {
+ StructureSelectionManager.getStructureSelectionManager(
+ Desktop.instance).addMappings(alignment.getCodonFrames());
+ }
}
/**
* DOCUMENT ME!
- *
- * @param state DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
*/
public void setWrapAlignment(boolean state)
{
@@ -919,8 +674,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param state DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
*/
public void setShowText(boolean state)
{
@@ -929,8 +685,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param state DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
*/
public void setRenderGaps(boolean state)
{
@@ -939,7 +696,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean getColourText()
@@ -949,8 +706,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param state DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
*/
public void setColourText(boolean state)
{
@@ -959,8 +717,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param state DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
*/
public void setShowBoxes(boolean state)
{
@@ -969,7 +728,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean getWrapAlignment()
@@ -979,7 +738,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean getShowText()
@@ -989,7 +748,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean getShowBoxes()
@@ -999,7 +758,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public char getGapCharacter()
@@ -1009,8 +768,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param gap DOCUMENT ME!
+ *
+ * @param gap
+ * DOCUMENT ME!
*/
public void setGapCharacter(char gap)
{
@@ -1022,47 +782,7 @@ public class AlignViewport
/**
* 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()
@@ -1072,8 +792,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param tree DOCUMENT ME!
+ *
+ * @param tree
+ * DOCUMENT ME!
*/
public void setCurrentTree(NJTree tree)
{
@@ -1082,7 +803,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public NJTree getCurrentTree()
@@ -1092,27 +813,7 @@ public class AlignViewport
/**
* 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()
@@ -1122,8 +823,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
*/
public void setShowJVSuffix(boolean b)
{
@@ -1132,7 +834,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean getShowAnnotation()
@@ -1142,8 +844,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
*/
public void setShowAnnotation(boolean b)
{
@@ -1152,7 +855,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean getScaleAboveWrapped()
@@ -1162,7 +865,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean getScaleLeftWrapped()
@@ -1172,7 +875,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean getScaleRightWrapped()
@@ -1182,8 +885,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
*/
public void setScaleAboveWrapped(boolean b)
{
@@ -1192,8 +896,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
*/
public void setScaleLeftWrapped(boolean b)
{
@@ -1202,64 +907,15 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param 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;
@@ -1270,535 +926,371 @@ public class AlignViewport
return isDataset;
}
- public void hideSelectedColumns()
+ public boolean getShowHiddenMarkers()
{
- if (colSel.size() < 1)
- {
- return;
- }
-
- colSel.hideSelectedColumns();
- setSelectionGroup(null);
+ return showHiddenMarkers;
+ }
- hasHiddenColumns = true;
+ public void setShowHiddenMarkers(boolean show)
+ {
+ showHiddenMarkers = show;
}
- public void hideColumns(int start, int end)
+ /**
+ * returns the visible column regions of the alignment
+ *
+ * @param selectedRegionOnly
+ * true to just return the contigs intersecting with the selected
+ * area
+ * @return
+ */
+ public int[] getViewAsVisibleContigs(boolean selectedRegionOnly)
{
- if (start == end)
+ int[] viscontigs = null;
+ int start = 0, end = 0;
+ if (selectedRegionOnly && selectionGroup != null)
{
- colSel.hideColumns(start);
+ start = selectionGroup.getStartRes();
+ end = selectionGroup.getEndRes() + 1;
}
else
{
- colSel.hideColumns(start, end);
+ end = alignment.getWidth();
}
-
- hasHiddenColumns = true;
+ viscontigs = colSel.getVisibleContigs(start, end);
+ return viscontigs;
}
- public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
+ /**
+ * get hash of undo and redo list for the alignment
+ *
+ * @return long[] { historyList.hashCode, redoList.hashCode };
+ */
+ public long[] getUndoRedoHash()
{
- int sSize = sg.getSize();
- if (sSize < 2)
+ // TODO: JAL-1126
+ if (historyList == null || redoList == null)
{
- return;
+ return new long[]
+ { -1, -1 };
}
+ return new long[]
+ { historyList.hashCode(), this.redoList.hashCode() };
+ }
- if (hiddenRepSequences == null)
+ /**
+ * 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)
{
- hiddenRepSequences = new Hashtable();
+ return true;
+ }
+ long[] cstate = getUndoRedoHash();
+ if (cstate.length != undoredo.length)
+ {
+ return true;
}
- 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++)
+ for (int i = 0; i < cstate.length; i++)
{
- if (sg.getSequenceAt(i) != repSequence)
+ if (cstate[i] != undoredo[i])
{
- if (index == sSize - 1)
- {
- return;
- }
-
- seqs[index++] = sg.getSequenceAt(i);
+ return true;
}
}
-
- hideSequence(seqs);
-
+ return false;
}
- public void hideAllSelectedSeqs()
+ public boolean getCentreColumnLabels()
{
- if (selectionGroup == null || selectionGroup.getSize()<1)
- {
- return;
- }
-
- SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
-
- hideSequence(seqs);
-
- setSelectionGroup(null);
+ return centreColumnLabels;
}
- public void hideSequence(SequenceI[] seq)
+ public void setCentreColumnLabels(boolean centrecolumnlabels)
{
- if (seq != null)
- {
- for (int i = 0; i < seq.length; i++)
- {
- alignment.getHiddenSequences().hideSequence(seq[i]);
- }
- hasHiddenRows = true;
- firePropertyChange("alignment", null, alignment.getSequences());
- }
+ centreColumnLabels = centrecolumnlabels;
}
- public void showSequence(int index)
+ /**
+ * enable or disable the display of Database Cross References in the sequence
+ * ID tooltip
+ */
+ public void setShowDbRefs(boolean show)
{
- 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());
- }
-
- if (alignment.getHiddenSequences().getSize() < 1)
- {
- hasHiddenRows = false;
- }
+ showdbrefs = show;
}
- public void showColumn(int col)
+ /**
+ *
+ * @return true if Database References are to be displayed on tooltips.
+ */
+ public boolean isShowDbRefs()
{
- colSel.revealHiddenColumns(col);
- if (colSel.getHiddenColumns() == null)
- {
- hasHiddenColumns = false;
- }
+ return showdbrefs;
}
- public void showAllHiddenColumns()
+ /**
+ *
+ * @return true if Non-positional features are to be displayed on tooltips.
+ */
+ public boolean isShowNpFeats()
{
- colSel.revealAllHiddenColumns();
- hasHiddenColumns = false;
+ return shownpfeats;
}
- public void showAllHiddenSeqs()
+ /**
+ * enable or disable the display of Non-Positional sequence features in the
+ * sequence ID tooltip
+ *
+ * @param show
+ */
+ public void setShowNpFeats(boolean show)
{
- 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());
- hasHiddenRows = false;
- hiddenRepSequences = null;
- }
+ shownpfeats = show;
}
- public void invertColumnSelection()
+ /**
+ *
+ * @return true if view has hidden rows
+ */
+ public boolean hasHiddenRows()
{
- for (int i = 0; i < alignment.getWidth(); i++)
- {
- if (colSel.contains(i))
- {
- colSel.removeElement(i);
- }
- else
- {
- if (!hasHiddenColumns || colSel.isVisible(i))
- {
- colSel.addElement(i);
- }
- }
- }
+ return hasHiddenRows;
}
- public int adjustForHiddenSeqs(int alignmentIndex)
+ /**
+ *
+ * @return true if view has hidden columns
+ */
+ public boolean hasHiddenColumns()
{
- return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
+ return hasHiddenColumns;
}
/**
- * This method returns the a new SequenceI [] with
- * the selection sequence and start and end points adjusted
- * @return String[]
+ * when set, view will scroll to show the highlighted position
*/
- public SequenceI[] getSelectionAsNewSequence()
- {
- SequenceI[] sequences;
+ public boolean followHighlight = true;
- if (selectionGroup == null)
- {
- sequences = alignment.getSequencesArray();
- }
- else
- {
- sequences = selectionGroup.getSelectionAsNewSequences(alignment);
- }
-
- return sequences;
+ /**
+ * @return true if view should scroll to show the highlighted region of a
+ * sequence
+ * @return
+ */
+ public boolean getFollowHighlight()
+ {
+ return followHighlight;
}
+ public boolean followSelection = true;
+
/**
- * 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[]
+ * @return true if view selection should always follow the selections
+ * broadcast by other selection sources
*/
- public jalview.datamodel.CigarArray getViewAsCigars(boolean
- selectedRegionOnly)
+ public boolean getFollowSelection()
{
- CigarArray 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(); // inclusive for start and end in SeqCigar constructor
- }
- else
- {
- iSize = alignment.getHeight();
- seqs = alignment.getSequencesArray();
- end = alignment.getWidth() - 1;
- }
- SeqCigar[] selseqs = new SeqCigar[iSize];
- for (i = 0; i < iSize; i++)
- {
- selseqs[i] = new SeqCigar(seqs[i], start, end);
- }
- selection = new CigarArray(selseqs);
- // now construct the CigarArray operations
- if (hasHiddenColumns)
- {
- Vector regions = colSel.getHiddenColumns();
- int[] region;
- int hideStart, hideEnd;
- int last = start;
- for (int j = 0; last < end & j < regions.size(); j++)
- {
- region = (int[]) regions.elementAt(j);
- hideStart = region[0];
- hideEnd = region[1];
- // edit hidden regions to selection range
- if (hideStart < last)
- {
- if (hideEnd > last)
- {
- hideStart = last;
- }
- else
- {
- continue;
- }
- }
+ return followSelection;
+ }
- if (hideStart > end)
- {
- break;
- }
+ boolean showSeqFeaturesHeight;
- if (hideEnd > end)
- {
- hideEnd = end;
- }
+ public void sendSelection()
+ {
+ jalview.structure.StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance).sendSelection(
+ new SequenceGroup(getSelectionGroup()),
+ new ColumnSelection(getColumnSelection()), this);
+ }
- if (hideStart > hideEnd)
- {
- break;
- }
- /**
- * form operations...
- */
- if (last < hideStart)
- {
- selection.addOperation(CigarArray.M, hideStart - last);
- }
- selection.addOperation(CigarArray.D, 1 + hideEnd - hideStart);
- last = hideEnd + 1;
- }
- // Final match if necessary.
- if (last < end)
- {
- selection.addOperation(CigarArray.M, end - last + 1);
- }
- }
- else
- {
- selection.addOperation(CigarArray.M, end - start + 1);
- }
- return selection;
+ public void setShowSequenceFeaturesHeight(boolean selected)
+ {
+ showSeqFeaturesHeight = selected;
+ }
+
+ public boolean getShowSequenceFeaturesHeight()
+ {
+ return showSeqFeaturesHeight;
}
/**
- * 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
+ * return the alignPanel containing the given viewport. Use this to get the
+ * components currently handling the given viewport.
+ *
+ * @param av
+ * @return null or an alignPanel guaranteed to have non-null alignFrame
+ * reference
*/
- jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly)
+ public AlignmentPanel getAlignPanel()
{
- // JBPNote:
- // this is here because the AlignmentView constructor modifies the CigarArray
- // object. Refactoring of Cigar and alignment view representation should
- // be done to remove redundancy.
- CigarArray aligview = getViewAsCigars(selectedOnly);
- if (aligview != null)
+ AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this
+ .getSequenceSetId());
+ AlignmentPanel ap = null;
+ for (int p = 0; aps != null && p < aps.length; p++)
{
- return new AlignmentView(aligview,
- (selectedOnly && selectionGroup != null) ?
- selectionGroup.getStartRes() : 0);
+ if (aps[p].av == this)
+ {
+ return aps[p];
+ }
}
return null;
}
+ public boolean getSortByTree()
+ {
+ return sortByTree;
+ }
+
+ public void setSortByTree(boolean sort)
+ {
+ sortByTree = sort;
+ }
+
/**
- * 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[]
+ * 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 String[] getViewAsString(boolean selectedRegionOnly)
+ public void expandColSelection(SequenceGroup sg, boolean wholewidth)
{
- 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)
+ int sgs, sge;
+ if (sg != null
+ && (sgs = sg.getStartRes()) >= 0
+ && sg.getStartRes() <= (sge = sg.getEndRes())
+ && (colSel == null || colSel.getSelected() == null || colSel
+ .getSelected().size() == 0))
{
- selection = colSel.getVisibleSequenceStrings(start, end, seqs);
- }
- else
- {
- for (i = 0; i < iSize; i++)
+ if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
{
- selection[i] = seqs[i].getSequenceAsString(start, end);
+ // do nothing
+ return;
+ }
+ if (colSel == null)
+ {
+ colSel = new ColumnSelection();
+ }
+ for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
+ {
+ colSel.addElement(cspos);
}
-
}
- return selection;
}
- public int [][] getVisibleRegionBoundaries(int min, int max)
+ public StructureSelectionManager getStructureSelectionManager()
{
- Vector regions = new Vector();
- int start = min;
- int end = max;
+ return StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ }
- do
+ /**
+ *
+ * @param pdbEntries
+ * @return a series of SequenceI arrays, one for each PDBEntry, listing which
+ * sequence in the alignment holds a reference to it
+ */
+ public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
+ {
+ ArrayList seqvectors = new ArrayList();
+ for (PDBEntry pdb : pdbEntries)
{
- if (hasHiddenColumns)
+ ArrayList seqs = new ArrayList();
+ for (int i = 0; i < alignment.getHeight(); i++)
{
- if (start == 0)
+ Vector pdbs = alignment.getSequenceAt(i).getDatasetSequence()
+ .getPDBId();
+ if (pdbs == null)
{
- start = colSel.adjustForHiddenColumns(start);
+ continue;
}
-
- end = colSel.getHiddenBoundaryRight(start);
- if (start == end)
- {
- end = max;
- }
- if (end > max)
+ SequenceI sq;
+ for (int p = 0; p < pdbs.size(); p++)
{
- end = max;
- }
- }
-
- regions.addElement(new int[]
- {start, end});
+ PDBEntry p1 = (PDBEntry) pdbs.elementAt(p);
+ if (p1.getId().equals(pdb.getId()))
+ {
+ if (!seqs.contains(sq = alignment.getSequenceAt(i)))
+ {
+ seqs.add(sq);
+ }
- if (hasHiddenColumns)
- {
- start = colSel.adjustForHiddenColumns(end);
- start = colSel.getHiddenBoundaryLeft(start) + 1;
+ continue;
+ }
+ }
}
+ seqvectors.add(seqs.toArray(new SequenceI[seqs.size()]));
}
- while (end < max);
-
- int[][] startEnd = new int[regions.size()][2];
-
- regions.copyInto(startEnd);
-
- return startEnd;
-
+ return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
}
- public boolean getShowHiddenMarkers()
+ public boolean isNormaliseSequenceLogo()
{
- return showHiddenMarkers;
+ return normaliseSequenceLogo;
}
- public void setShowHiddenMarkers(boolean show)
+ public void setNormaliseSequenceLogo(boolean state)
{
- showHiddenMarkers = show;
+ normaliseSequenceLogo = state;
}
- public String getSequenceSetId()
+ /**
+ *
+ * @return true if alignment characters should be displayed
+ */
+ public boolean isValidCharWidth()
{
- if (sequenceSetID == null)
- {
- sequenceSetID = alignment.hashCode() + "";
- }
-
- return sequenceSetID;
+ return validCharWidth;
}
- public void alignmentChanged(AlignmentPanel ap)
- {
- if (padGaps)
- {
- alignment.padGaps();
- }
+ private Hashtable calcIdParams = new Hashtable();
- if (hconsensus != null && autoCalculateConsensus)
- {
- updateConsensus(ap);
- updateConservation(ap);
- }
+ private boolean showAutocalculatedAbove;
- //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();
+ public AutoCalcSetting getCalcIdSettingsFor(String calcId)
+ {
+ return calcIdParams.get(calcId);
}
- void resetAllColourSchemes()
+ public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings,
+ boolean needsUpdate)
{
- 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++)
+ 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)
{
- 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();
+ Cache.log.debug("trigger update for " + calcId);
}
}
- public Color getSequenceColour(SequenceI seq)
+ protected SequenceAnnotationOrder getSortAnnotationsBy()
{
- if (sequenceColours == null || !sequenceColours.containsKey(seq))
- {
- return Color.white;
- }
- else
- {
- return (Color) sequenceColours.get(seq);
- }
+ return sortAnnotationsBy;
}
- public void setSequenceColour(SequenceI seq, Color col)
+ protected void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy)
{
- if (sequenceColours == null)
- {
- sequenceColours = new Hashtable();
- }
+ this.sortAnnotationsBy = sortAnnotationsBy;
+ }
- if (col == null)
- {
- sequenceColours.remove(seq);
- }
- else
- {
- sequenceColours.put(seq, col);
- }
+ protected boolean isShowAutocalculatedAbove()
+ {
+ return showAutocalculatedAbove;
}
+ protected void setShowAutocalculatedAbove(boolean showAutocalculatedAbove)
+ {
+ this.showAutocalculatedAbove = showAutocalculatedAbove;
+ }
}