X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=f5bc6e4cf3014e61522070c5bffd4270d833be39;hb=7aa643222eefde760ffe621bc1e04ca50713f66e;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..f5bc6e4
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,4 +1,21 @@
/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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 .
+ */
+/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
@@ -23,72 +40,130 @@ import java.util.*;
import java.awt.*;
import jalview.analysis.*;
+import jalview.api.StructureSelectionManagerProvider;
+
import jalview.bin.*;
+
import jalview.datamodel.*;
+
import jalview.schemes.*;
+import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
- * @version $Revision$
+ * @version $Revision: 1.141 $
*/
-public class AlignViewport
+public class AlignViewport implements SelectionSource, VamsasSource
{
+ private static final int RIGHT_JUSTIFY = 1;
+
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;
+
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;
+
+ public Hashtable[] hStrucConsensus;
+
AlignmentAnnotation consensus;
+
+ AlignmentAnnotation strucConsensus;
+
AlignmentAnnotation conservation;
+
AlignmentAnnotation quality;
+
+ AlignmentAnnotation[] groupConsensus;
+
+ AlignmentAnnotation[] groupConservation;
+
boolean autoCalculateConsensus = true;
+ boolean autoCalculateStrucConsensus = 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);
+ private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
+ this);
boolean ignoreGapsInConsensusCalculation = false;
@@ -107,22 +182,28 @@ public class AlignViewport
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;
+
/**
* Creates a new AlignViewport object.
- *
- * @param al DOCUMENT ME!
+ *
+ * @param al
+ * alignment to view
*/
public AlignViewport(AlignmentI al)
{
@@ -131,9 +212,42 @@ 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 +255,71 @@ 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 +337,12 @@ 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);
+ 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 +363,8 @@ 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
@@ -195,11 +373,9 @@ 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 of total alignment less than " + ConsPercGaps
+ + "% gaps", new Annotation[1], 0f, 11f,
+ AlignmentAnnotation.BAR_GRAPH);
conservation.hasText = true;
conservation.autoCalculated = true;
@@ -211,40 +387,62 @@ public class AlignViewport
if (Cache.getDefault("SHOW_QUALITY", true))
{
quality = new AlignmentAnnotation("Quality",
- "Alignment Quality based on Blosum62 scores",
- new Annotation[1],
- 0f,
- 11f,
- AlignmentAnnotation.BAR_GRAPH);
+ "Alignment Quality based on Blosum62 scores",
+ new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
quality.hasText = true;
quality.autoCalculated = true;
alignment.addAnnotation(quality);
}
- }
+ showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
+ false);
+ {
+
+ }
+ }
+ showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
+ true);
+ showSequenceLogo = Cache.getDefault("SHOW_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);
+ new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
consensus.hasText = true;
consensus.autoCalculated = true;
+ if (alignment.isNucleotide() && alignment.hasRNAStructure())
+ {
+ strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
+ new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
+ strucConsensus.hasText = true;
+ strucConsensus.autoCalculated = true;
+ }
+
if (Cache.getDefault("SHOW_IDENTITY", true))
{
alignment.addAnnotation(consensus);
+ // TODO: Make own if for structure
+ if (alignment.isNucleotide() && alignment.hasRNAStructure())
+ {
+ alignment.addAnnotation(strucConsensus);
+ }
}
+
}
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)
@@ -254,12 +452,18 @@ public class AlignViewport
}
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);
}
/**
- * DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
+ * set the flag
+ *
+ * @param b
+ * features are displayed if true
*/
public void setShowSequenceFeatures(boolean b)
{
@@ -271,207 +475,70 @@ 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;
+ StrucConsensusThread strucConsensusThread;
+
boolean consUpdateNeeded = false;
static boolean UPDATING_CONSENSUS = false;
+ static boolean UPDATING_STRUC_CONSENSUS = false;
+
static boolean UPDATING_CONSERVATION = false;
boolean updatingConsensus = false;
+ boolean updatingStrucConsensus = false;
+
boolean updatingConservation = false;
/**
- * DOCUMENT ME!
+ * 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)
{
- if (alignment.isNucleotide() || conservation == null)
+ // see note in mantis : issue number 8585
+ if (alignment.isNucleotide() || conservation == null
+ || !autoCalculateConsensus)
{
return;
}
- conservationThread = new ConservationThread(ap);
+ conservationThread = new ConservationThread(this, ap);
conservationThread.start();
}
/**
- * DOCUMENT ME!
+ * 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
+ class ConsensusThread extends Thread
{
AlignmentPanel ap;
+
public ConsensusThread(AlignmentPanel ap)
{
this.ap = ap;
@@ -486,12 +553,11 @@ public class AlignViewport
{
if (ap != null)
{
- ap.paintAlignment(true);
+ ap.paintAlignment(false);
}
Thread.sleep(200);
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
@@ -501,9 +567,14 @@ public class AlignViewport
try
{
- int aWidth = alignment.getWidth();
- if (aWidth < 0)
+ int aWidth = (alignment != null) ? alignment.getWidth() : -1; // null
+ // pointer
+ // possibility
+ // here.
+ if (aWidth <= 0)
{
+ updatingConsensus = false;
+ UPDATING_CONSENSUS = false;
return;
}
@@ -511,66 +582,21 @@ public class AlignViewport
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);
- }
-
+ AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment
+ .getWidth(), hconsensus, true);
+ updateAnnotation(true);
if (globalColourScheme != null)
{
globalColourScheme.setConsensus(hconsensus);
}
- }
- catch (OutOfMemoryError error)
+ } 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);
- }
- });
-
- System.out.println("Consensus calculation: " + error);
- System.gc();
+ new OOMWarning("calculating consensus", error);
}
UPDATING_CONSENSUS = false;
updatingConsensus = false;
@@ -580,59 +606,209 @@ public class AlignViewport
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);
+ }
+ }
}
- /**
- * get the consensus sequence as displayed under the PID consensus annotation row.
- * @return consensus sequence as a new sequence object
- */
- public SequenceI getConsensusSeq()
+ // --------START Structure Conservation
+ public void updateStrucConsensus(final AlignmentPanel ap)
{
- if (consensus == null)
+ // see note in mantis : issue number 8585
+ if (strucConsensus == null || !autoCalculateStrucConsensus)
{
- updateConsensus(null);
+ return;
}
- if (consensus == null)
+ strucConsensusThread = new StrucConsensusThread(ap);
+ strucConsensusThread.start();
+ }
+
+ class StrucConsensusThread extends Thread
+ {
+ AlignmentPanel ap;
+
+ public StrucConsensusThread(AlignmentPanel ap)
{
- return null;
+ this.ap = ap;
}
- StringBuffer seqs = new StringBuffer();
- for (int i = 0; i < consensus.annotations.length; i++)
+
+ public void run()
{
- if (consensus.annotations[i] != null)
+ updatingStrucConsensus = true;
+ while (UPDATING_STRUC_CONSENSUS)
{
- if (consensus.annotations[i].description.charAt(0) == '[')
+ try
{
- seqs.append(consensus.annotations[i].description.charAt(1));
- }
- else
+ if (ap != null)
+ {
+ ap.paintAlignment(false);
+ }
+
+ Thread.sleep(200);
+ } catch (Exception ex)
{
- seqs.append(consensus.annotations[i].displayCharacter);
+ ex.printStackTrace();
}
}
- }
- SequenceI sq = new Sequence("Consensus", seqs.toString());
- sq.setDescription("Percentage Identity Consensus " +
- ( (ignoreGapsInConsensusCalculation) ? " without gaps" :
- ""));
- return sq;
- }
+ UPDATING_STRUC_CONSENSUS = true;
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public SequenceGroup getSelectionGroup()
+ try
+ {
+ int aWidth = (alignment != null) ? alignment.getWidth() : -1; // null
+ // pointer
+ // possibility
+ // here.
+ if (aWidth <= 0)
+ {
+ updatingStrucConsensus = false;
+ UPDATING_STRUC_CONSENSUS = false;
+ return;
+ }
+
+ strucConsensus.annotations = null;
+ strucConsensus.annotations = new Annotation[aWidth];
+
+ hStrucConsensus = new Hashtable[aWidth];
+
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
+ AlignmentAnnotation rnaStruc = null;
+ for (int i = 0; i < aa.length; i++)
+ {
+ if (aa[i].getRNAStruc() != null)
+ {
+ rnaStruc = aa[i];
+ break;
+ }
+ }
+
+ AlignmentAnnotation rna = ap.av.getAlignment()
+ .getAlignmentAnnotation()[0];
+ StructureFrequency.calculate(alignment.getSequencesArray(), 0,
+ alignment.getWidth(), hStrucConsensus, true, rnaStruc);
+ // TODO AlignmentAnnotation rnaStruc!!!
+ updateAnnotation(true);
+ if (globalColourScheme != null)
+ {
+ globalColourScheme.setConsensus(hStrucConsensus);
+ }
+
+ } catch (OutOfMemoryError error)
+ {
+ alignment.deleteAnnotation(strucConsensus);
+
+ strucConsensus = null;
+ hStrucConsensus = null;
+ new OOMWarning("calculating structure consensus", error);
+ }
+ UPDATING_STRUC_CONSENSUS = false;
+ updatingStrucConsensus = 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
+ || (!updatingStrucConsensus && strucConsensus != null && hStrucConsensus != null))
+ {
+ StructureFrequency.completeConsensus(strucConsensus,
+ hStrucConsensus, 0, hStrucConsensus.length, false,
+ showSequenceLogo);
+ }
+ }
+ }
+
+ // --------END Structure Conservation
+
+ /**
+ * get the consensus sequence as displayed under the PID consensus annotation
+ * row.
+ *
+ * @return consensus sequence as a new sequence object
+ */
+ public SequenceI getConsensusSeq()
+ {
+ if (consensus == null)
+ {
+ updateConsensus(null);
+ }
+ if (consensus == null)
+ {
+ return null;
+ }
+ StringBuffer seqs = new StringBuffer();
+ for (int i = 0; i < consensus.annotations.length; i++)
+ {
+ if (consensus.annotations[i] != null)
+ {
+ if (consensus.annotations[i].description.charAt(0) == '[')
+ {
+ seqs.append(consensus.annotations[i].description.charAt(1));
+ }
+ else
+ {
+ seqs.append(consensus.annotations[i].displayCharacter);
+ }
+ }
+ }
+
+ SequenceI sq = new Sequence("Consensus", seqs.toString());
+ sq.setDescription("Percentage Identity Consensus "
+ + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
+ return sq;
+ }
+
+ /**
+ *
+ *
+ * @return null or the currently selected sequence region
+ */
+ public SequenceGroup getSelectionGroup()
{
return selectionGroup;
}
/**
- * DOCUMENT ME!
- *
- * @param sg DOCUMENT ME!
+ * Set the selection group for this window.
+ *
+ * @param sg
+ * - group holding references to sequences in this alignment view
+ *
*/
public void setSelectionGroup(SequenceGroup sg)
{
@@ -640,9 +816,9 @@ public class AlignViewport
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * GUI state
+ *
+ * @return true if conservation based shading is enabled
*/
public boolean getConservationSelected()
{
@@ -650,9 +826,10 @@ public class AlignViewport
}
/**
- * DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
+ * GUI state
+ *
+ * @param b
+ * enable conservation based shading
*/
public void setConservationSelected(boolean b)
{
@@ -660,9 +837,9 @@ public class AlignViewport
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * GUI state
+ *
+ * @return true if percent identity threshold is applied to shading
*/
public boolean getAbovePIDThreshold()
{
@@ -670,9 +847,11 @@ public class AlignViewport
}
/**
- * DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
+ * GUI state
+ *
+ *
+ * @param b
+ * indicate if percent identity threshold is applied to shading
*/
public void setAbovePIDThreshold(boolean b)
{
@@ -681,7 +860,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getStartRes()
@@ -691,7 +870,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getEndRes()
@@ -701,7 +880,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getStartSeq()
@@ -711,8 +890,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param cs DOCUMENT ME!
+ *
+ * @param cs
+ * DOCUMENT ME!
*/
public void setGlobalColourScheme(ColourSchemeI cs)
{
@@ -721,7 +901,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public ColourSchemeI getGlobalColourScheme()
@@ -731,8 +911,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param res DOCUMENT ME!
+ *
+ * @param res
+ * DOCUMENT ME!
*/
public void setStartRes(int res)
{
@@ -741,8 +922,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param seq DOCUMENT ME!
+ *
+ * @param seq
+ * DOCUMENT ME!
*/
public void setStartSeq(int seq)
{
@@ -751,14 +933,16 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param res 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));
+ // log.System.out.println(" Corrected res from " + res + " to maximum " +
+ // (alignment.getWidth()-1));
res = alignment.getWidth() - 1;
}
@@ -772,8 +956,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param seq DOCUMENT ME!
+ *
+ * @param seq
+ * DOCUMENT ME!
*/
public void setEndSeq(int seq)
{
@@ -792,7 +977,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getEndSeq()
@@ -802,8 +987,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param f DOCUMENT ME!
+ *
+ * @param f
+ * DOCUMENT ME!
*/
public void setFont(Font f)
{
@@ -819,7 +1005,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public Font getFont()
@@ -829,8 +1015,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param w DOCUMENT ME!
+ *
+ * @param w
+ * DOCUMENT ME!
*/
public void setCharWidth(int w)
{
@@ -839,7 +1026,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getCharWidth()
@@ -849,8 +1036,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param h DOCUMENT ME!
+ *
+ * @param h
+ * DOCUMENT ME!
*/
public void setCharHeight(int h)
{
@@ -859,7 +1047,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getCharHeight()
@@ -869,8 +1057,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param w DOCUMENT ME!
+ *
+ * @param w
+ * DOCUMENT ME!
*/
public void setWrappedWidth(int w)
{
@@ -879,7 +1068,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getWrappedWidth()
@@ -889,7 +1078,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public AlignmentI getAlignment()
@@ -899,18 +1088,30 @@ 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.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 +1120,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param state DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
*/
public void setShowText(boolean state)
{
@@ -929,8 +1131,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param state DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
*/
public void setRenderGaps(boolean state)
{
@@ -939,7 +1142,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean getColourText()
@@ -949,8 +1152,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param state DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
*/
public void setColourText(boolean state)
{
@@ -959,8 +1163,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param state DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
*/
public void setShowBoxes(boolean state)
{
@@ -969,7 +1174,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean getWrapAlignment()
@@ -979,7 +1184,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean getShowText()
@@ -989,7 +1194,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean getShowBoxes()
@@ -999,7 +1204,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public char getGapCharacter()
@@ -1009,8 +1214,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param gap DOCUMENT ME!
+ *
+ * @param gap
+ * DOCUMENT ME!
*/
public void setGapCharacter(char gap)
{
@@ -1022,8 +1228,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param thresh DOCUMENT ME!
+ *
+ * @param thresh
+ * DOCUMENT ME!
*/
public void setThreshold(int thresh)
{
@@ -1032,7 +1239,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getThreshold()
@@ -1042,8 +1249,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param inc DOCUMENT ME!
+ *
+ * @param inc
+ * DOCUMENT ME!
*/
public void setIncrement(int inc)
{
@@ -1052,7 +1260,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getIncrement()
@@ -1062,7 +1270,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public ColumnSelection getColumnSelection()
@@ -1072,8 +1280,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param tree DOCUMENT ME!
+ *
+ * @param tree
+ * DOCUMENT ME!
*/
public void setCurrentTree(NJTree tree)
{
@@ -1082,7 +1291,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public NJTree getCurrentTree()
@@ -1092,8 +1301,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
*/
public void setColourAppliesToAllGroups(boolean b)
{
@@ -1102,7 +1312,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean getColourAppliesToAllGroups()
@@ -1112,7 +1322,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean getShowJVSuffix()
@@ -1122,8 +1332,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
*/
public void setShowJVSuffix(boolean b)
{
@@ -1132,7 +1343,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean getShowAnnotation()
@@ -1142,8 +1353,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
*/
public void setShowAnnotation(boolean b)
{
@@ -1152,7 +1364,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean getScaleAboveWrapped()
@@ -1162,7 +1374,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean getScaleLeftWrapped()
@@ -1172,7 +1384,7 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean getScaleRightWrapped()
@@ -1182,8 +1394,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
*/
public void setScaleAboveWrapped(boolean b)
{
@@ -1192,8 +1405,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
*/
public void setScaleLeftWrapped(boolean b)
{
@@ -1202,8 +1416,9 @@ public class AlignViewport
/**
* DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
*/
public void setScaleRightWrapped(boolean b)
{
@@ -1212,34 +1427,40 @@ public class AlignViewport
/**
* Property change listener for changes in alignment
- *
- * @param listener DOCUMENT ME!
+ *
+ * @param listener
+ * DOCUMENT ME!
*/
public void addPropertyChangeListener(
- java.beans.PropertyChangeListener listener)
+ java.beans.PropertyChangeListener listener)
{
changeSupport.addPropertyChangeListener(listener);
}
/**
* DOCUMENT ME!
- *
- * @param listener DOCUMENT ME!
+ *
+ * @param listener
+ * DOCUMENT ME!
*/
public void removePropertyChangeListener(
- java.beans.PropertyChangeListener listener)
+ 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!
+ *
+ * @param prop
+ * DOCUMENT ME!
+ * @param oldvalue
+ * DOCUMENT ME!
+ * @param newvalue
+ * DOCUMENT ME!
*/
- public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
+ public void firePropertyChange(String prop, Object oldvalue,
+ Object newvalue)
{
changeSupport.firePropertyChange(prop, oldvalue, newvalue);
}
@@ -1251,7 +1472,7 @@ public class AlignViewport
if (globalColourScheme != null)
{
globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
- ignoreGapsInConsensusCalculation);
+ ignoreGapsInConsensusCalculation);
}
}
@@ -1312,7 +1533,7 @@ public class AlignViewport
hiddenRepSequences.put(repSequence, sg);
- //Hide all sequences except the repSequence
+ // Hide all sequences except the repSequence
SequenceI[] seqs = new SequenceI[sSize - 1];
int index = 0;
for (int i = 0; i < sSize; i++)
@@ -1327,14 +1548,15 @@ public class AlignViewport
seqs[index++] = sg.getSequenceAt(i);
}
}
-
+ sg.setSeqrep(repSequence);
+ sg.setHidereps(true);
hideSequence(seqs);
}
public void hideAllSelectedSeqs()
{
- if (selectionGroup == null || selectionGroup.getSize()<1)
+ if (selectionGroup == null || selectionGroup.getSize() < 1)
{
return;
}
@@ -1361,8 +1583,8 @@ public class AlignViewport
public void showSequence(int index)
{
- Vector tmp = alignment.getHiddenSequences().showSequence(index
- , hiddenRepSequences);
+ Vector tmp = alignment.getHiddenSequences().showSequence(index,
+ hiddenRepSequences);
if (tmp.size() > 0)
{
if (selectionGroup == null)
@@ -1373,11 +1595,10 @@ public class AlignViewport
for (int t = 0; t < tmp.size(); t++)
{
- selectionGroup.addSequence(
- (SequenceI) tmp.elementAt(t), false
- );
+ selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
}
firePropertyChange("alignment", null, alignment.getSequences());
+ sendSelection();
}
if (alignment.getHiddenSequences().getSize() < 1)
@@ -1410,14 +1631,14 @@ public class AlignViewport
selectionGroup = new SequenceGroup();
selectionGroup.setEndRes(alignment.getWidth() - 1);
}
- Vector tmp = alignment.getHiddenSequences().showAll(hiddenRepSequences);
+ Vector tmp = alignment.getHiddenSequences().showAll(
+ hiddenRepSequences);
for (int t = 0; t < tmp.size(); t++)
{
- selectionGroup.addSequence(
- (SequenceI) tmp.elementAt(t), false
- );
+ selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
}
firePropertyChange("alignment", null, alignment.getSequences());
+ sendSelection();
hasHiddenRows = false;
hiddenRepSequences = null;
}
@@ -1425,31 +1646,23 @@ public class AlignViewport
public void invertColumnSelection()
{
- for (int i = 0; i < alignment.getWidth(); i++)
- {
- if (colSel.contains(i))
- {
- colSel.removeElement(i);
- }
- else
- {
- if (!hasHiddenColumns || colSel.isVisible(i))
- {
- colSel.addElement(i);
- }
- }
- }
+ colSel.invertColumnSelection(0, alignment.getWidth());
}
public int adjustForHiddenSeqs(int alignmentIndex)
{
- return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
+ return alignment.getHiddenSequences().adjustForHiddenSeqs(
+ alignmentIndex);
}
/**
- * This method returns the a new SequenceI [] with
- * the selection sequence and start and end points adjusted
- * @return String[]
+ * 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()
{
@@ -1458,6 +1671,14 @@ public class AlignViewport
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
{
@@ -1468,129 +1689,80 @@ public class AlignViewport
}
/**
- * 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[]
+ * get the currently selected sequence objects or all the sequences in the
+ * alignment.
+ *
+ * @return array of references to sequence objects
*/
- public jalview.datamodel.CigarArray getViewAsCigars(boolean
- selectedRegionOnly)
+ public SequenceI[] getSequenceSelection()
{
- CigarArray selection = null;
- SequenceI[] seqs = null;
- int i, iSize;
- int start = 0, end = 0;
- if (selectedRegionOnly && selectionGroup != null)
+ SequenceI[] sequences = null;
+ if (selectionGroup != null)
{
- iSize = selectionGroup.getSize();
- seqs = selectionGroup.getSequencesInOrder(alignment);
- start = selectionGroup.getStartRes();
- end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
+ sequences = selectionGroup.getSequencesInOrder(alignment);
}
- else
+ if (sequences == null)
{
- 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);
+ sequences = alignment.getSequencesArray();
}
- 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;
- }
- }
-
- if (hideStart > end)
- {
- break;
- }
+ return sequences;
+ }
- if (hideEnd > end)
- {
- hideEnd = end;
- }
+ /**
+ * 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));
+ }
- 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;
+ /**
+ * 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
- * @param selectedOnly boolean true to just return the selected view
+ * 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
+ * @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
*/
- jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly)
+ public jalview.datamodel.AlignmentView getAlignmentView(
+ boolean selectedOnly, boolean markGroups)
{
- // 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)
- {
- return new AlignmentView(aligview,
- (selectedOnly && selectionGroup != null) ?
- selectionGroup.getStartRes() : 0);
- }
- return null;
+ return new AlignmentView(alignment, colSel, selectionGroup,
+ hasHiddenColumns, selectedOnly, markGroups);
}
/**
- * 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.
+ * 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 String[] getViewAsString(boolean selectedRegionOnly)
@@ -1629,7 +1801,7 @@ public class AlignViewport
return selection;
}
- public int [][] getVisibleRegionBoundaries(int min, int max)
+ public int[][] getVisibleRegionBoundaries(int min, int max)
{
Vector regions = new Vector();
int start = min;
@@ -1656,15 +1828,14 @@ public class AlignViewport
}
regions.addElement(new int[]
- {start, end});
+ { start, end });
if (hasHiddenColumns)
{
start = colSel.adjustForHiddenColumns(end);
start = colSel.getHiddenBoundaryLeft(start) + 1;
}
- }
- while (end < max);
+ } while (end < max);
int[][] startEnd = new int[regions.size()][2];
@@ -1694,20 +1865,41 @@ public class AlignViewport
return sequenceSetID;
}
+ /**
+ * unique viewId for synchronizing state with stored Jalview Project
+ *
+ */
+ 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)
{
- updateConsensus(ap);
updateConservation(ap);
}
+ if (autoCalculateConsensus)
+ {
+ updateConsensus(ap);
+ }
+ if (autoCalculateStrucConsensus)
+ {
+ updateStrucConsensus(ap);
+ }
- //Reset endRes of groups if beyond alignment width
+ // Reset endRes of groups if beyond alignment width
int alWidth = alignment.getWidth();
Vector groups = alignment.getGroups();
if (groups != null)
@@ -1739,9 +1931,8 @@ public class AlignViewport
{
if (cs instanceof ClustalxColourScheme)
{
- ( (ClustalxColourScheme) cs).
- resetClustalX(alignment.getSequences(),
- alignment.getWidth());
+ ((ClustalxColourScheme) cs).resetClustalX(alignment.getSequences(),
+ alignment.getWidth());
}
cs.setConsensus(hconsensus);
@@ -1749,9 +1940,8 @@ public class AlignViewport
{
Alignment al = (Alignment) alignment;
Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3,
- al.getSequences(), 0,
- al.getWidth() - 1);
+ ResidueProperties.propHash, 3, al.getSequences(), 0, al
+ .getWidth() - 1);
c.calculate();
c.verdict(false, ConsPercGaps);
@@ -1765,8 +1955,8 @@ public class AlignViewport
SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s);
if (sg.cs != null && sg.cs instanceof ClustalxColourScheme)
{
- ( (ClustalxColourScheme) sg.cs).resetClustalX(
- sg.getSequences(hiddenRepSequences), sg.getWidth());
+ ((ClustalxColourScheme) sg.cs).resetClustalX(sg
+ .getSequences(hiddenRepSequences), sg.getWidth());
}
sg.recalcConservation();
}
@@ -1801,4 +1991,479 @@ public class AlignViewport
}
}
+ /**
+ * 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)
+ {
+ int[] viscontigs = null;
+ int start = 0, end = 0;
+ if (selectedRegionOnly && selectionGroup != null)
+ {
+ start = selectionGroup.getStartRes();
+ end = selectionGroup.getEndRes() + 1;
+ }
+ else
+ {
+ 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 true if view has hidden rows
+ */
+ public boolean hasHiddenRows()
+ {
+ return hasHiddenRows;
+ }
+
+ /**
+ *
+ * @return true if view has hidden columns
+ */
+ public boolean hasHiddenColumns()
+ {
+ return hasHiddenColumns;
+ }
+
+ /**
+ * when set, view will scroll to show the highlighted position
+ */
+ public boolean followHighlight = true;
+
+ /**
+ * @return true if view should scroll to show the highlighted region of a
+ * sequence
+ * @return
+ */
+ public boolean getFollowHighlight()
+ {
+ return followHighlight;
+ }
+
+ public boolean followSelection = true;
+
+ /**
+ * @return true if view selection should always follow the selections
+ * broadcast by other selection sources
+ */
+ public boolean getFollowSelection()
+ {
+ 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)
+ */
+ 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
+ .getStructureSelectionManager(Desktop.instance).sendSelection(
+ new SequenceGroup(getSelectionGroup()),
+ 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.
+ *
+ * @param av
+ * @return null or an alignPanel guaranteed to have non-null alignFrame
+ * reference
+ */
+ public AlignmentPanel getAlignPanel()
+ {
+ AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this
+ .getSequenceSetId());
+ AlignmentPanel ap = null;
+ for (int p = 0; aps != null && p < aps.length; p++)
+ {
+ if (aps[p].av == this)
+ {
+ return aps[p];
+ }
+ }
+ return null;
+ }
+
+ public boolean getSortByTree()
+ {
+ return sortByTree;
+ }
+
+ public void setSortByTree(boolean sort)
+ {
+ sortByTree = sort;
+ }
+
+ /**
+ * 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
+ */
+ public boolean showConsensusHistogram = true;
+
+ /**
+ * @return the showConsensusProfile
+ */
+ public boolean isShowSequenceLogo()
+ {
+ return showSequenceLogo;
+ }
+
+ /**
+ * @param showSequenceLogo
+ * the new value
+ */
+ public void setShowSequenceLogo(boolean showSequenceLogo)
+ {
+ if (showSequenceLogo != this.showSequenceLogo)
+ {
+ // TODO: decouple settings setting from calculation when refactoring
+ // annotation update method from alignframe to viewport
+ this.showSequenceLogo = showSequenceLogo;
+ if (consensusThread != null)
+ {
+ consensusThread.updateAnnotation();
+ }
+ if (strucConsensusThread != null)
+ {
+ strucConsensusThread.updateAnnotation();
+ }
+ }
+ this.showSequenceLogo = showSequenceLogo;
+ }
+
+ /**
+ * @param showConsensusHistogram
+ * the showConsensusHistogram to set
+ */
+ public void setShowConsensusHistogram(boolean showConsensusHistogram)
+ {
+ this.showConsensusHistogram = showConsensusHistogram;
+ }
+
+ /**
+ * @return the showGroupConservation
+ */
+ public boolean isShowGroupConservation()
+ {
+ return showGroupConservation;
+ }
+
+ /**
+ * @param showGroupConservation
+ * the showGroupConservation to set
+ */
+ public void setShowGroupConservation(boolean showGroupConservation)
+ {
+ this.showGroupConservation = showGroupConservation;
+ }
+
+ /**
+ * @return the showGroupConsensus
+ */
+ public boolean isShowGroupConsensus()
+ {
+ return showGroupConsensus;
+ }
+
+ /**
+ * @param showGroupConsensus
+ * the showGroupConsensus to set
+ */
+ public void setShowGroupConsensus(boolean showGroupConsensus)
+ {
+ this.showGroupConsensus = showGroupConsensus;
+ }
+
+ /**
+ *
+ * @return flag to indicate if the consensus histogram should be rendered by
+ * default
+ */
+ public boolean isShowConsensusHistogram()
+ {
+ return this.showConsensusHistogram;
+ }
+
+ /**
+ * 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 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);
+ }
+ }
+ }
+
+ public StructureSelectionManager getStructureSelectionManager()
+ {
+ return StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ }
+
+ /**
+ *
+ * @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)
+ {
+ ArrayList seqs = new ArrayList();
+ for (int i = 0; i < alignment.getHeight(); i++)
+ {
+ 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()]));
+ }
+ return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
+ }
}