- /*
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ */
+/*
* Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
*/
package jalview.gui;
+import java.util.*;
+
+import java.awt.*;
+
import jalview.analysis.*;
+import jalview.api.StructureSelectionManagerProvider;
import jalview.bin.*;
import jalview.datamodel.*;
import jalview.schemes.*;
-
-import java.awt.*;
-
-import java.util.*;
-
+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
{
- 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;
- 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;
+ private static final int RIGHT_JUSTIFY = 1;
- // The following vector holds the features which are
- // currently visible, in the correct order or rendering
- Hashtable featuresDisplayed = null;
+ int startRes;
+ int endRes;
- /** DOCUMENT ME!! */
- public Hashtable [] hconsensus;
- AlignmentAnnotation consensus;
- AlignmentAnnotation conservation;
- AlignmentAnnotation quality;
- boolean autoCalculateConsensus = true;
+ int startSeq;
- /** DOCUMENT ME!! */
- public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
+ int endSeq;
- // JBPNote Prolly only need this in the applet version.
- private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
+ boolean showJVSuffix = true;
- boolean ignoreGapsInConsensusCalculation = false;
+ boolean showText = true;
- boolean isDataset = false;
+ boolean showColourText = false;
- boolean antiAlias = false;
+ boolean showBoxes = true;
- boolean padGaps = false;
+ boolean wrapAlignment = false;
- Rectangle explodedPosition;
+ boolean renderGaps = true;
- String viewName;
+ boolean showSequenceFeatures = false;
- String sequenceSetID;
+ boolean showAnnotation = true;
- boolean gatherViewsHere = false;
+ boolean colourAppliesToAllGroups = true;
- Stack historyList = new Stack();
- Stack redoList = new Stack();
+ ColourSchemeI globalColourScheme = null;
- Hashtable sequenceColours;
+ boolean conservationColourSelected = false;
- int thresholdTextColour = 0;
- Color textColour = Color.black;
- Color textColour2 = Color.white;
-
- boolean idsAlignRight = false;
-
-
- /**
- * Creates a new AlignViewport object.
- *
- * @param al DOCUMENT ME!
- */
- public AlignViewport(AlignmentI al)
- {
- setAlignment(al);
- init();
- }
- /**
- * Create a new AlignViewport with hidden regions
- * @param al AlignmentI
- * @param hiddenColumns ColumnSelection
- */
- public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns) {
- setAlignment(al);
- if (hiddenColumns!=null) {
- this.colSel = hiddenColumns;
- if (hiddenColumns.getHiddenColumns() != null)
- hasHiddenColumns = true;
- }
- init();
- }
+ boolean abovePIDThreshold = false;
- void init()
- {
- this.startRes = 0;
- this.endRes = alignment.getWidth() - 1;
- this.startSeq = 0;
- this.endSeq = alignment.getHeight() - 1;
+ SequenceGroup selectionGroup;
- antiAlias = Cache.getDefault("ANTI_ALIAS", false);
+ int charHeight;
- showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
- showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
+ int charWidth;
- autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
+ boolean validCharWidth;
- padGaps = Cache.getDefault("PAD_GAPS", true);
+ int wrappedWidth;
- String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
- String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
- String fontSize = Cache.getDefault("FONT_SIZE", "10");
+ Font font;
- int style = 0;
+ boolean seqNameItalics;
- if (fontStyle.equals("bold"))
- {
- style = 1;
- }
- else if (fontStyle.equals("italic"))
- {
- style = 2;
- }
+ AlignmentI alignment;
- setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
+ ColumnSelection colSel = new ColumnSelection();
- alignment.setGapCharacter( Cache.getDefault("GAP_SYMBOL", "-").charAt(0) );
+ int threshold;
+ int increment;
- // We must set conservation and consensus before setting colour,
- // as Blosum and Clustal require this to be done
- if(hconsensus==null && !isDataset)
- {
- 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;
-
-
- 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;
-
- alignment.addAnnotation(quality);
- }
- }
+ NJTree currentTree = null;
- consensus = new AlignmentAnnotation("Consensus", "PID",
- new Annotation[1], 0f, 100f,
- AlignmentAnnotation.BAR_GRAPH);
- consensus.hasText = true;
+ boolean scaleAboveWrapped = false;
- if (Cache.getDefault("SHOW_IDENTITY", true))
- {
- alignment.addAnnotation(consensus);
- }
- }
+ boolean scaleLeftWrapped = true;
- if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
- {
- globalColourScheme = ColourSchemeProperty.getColour(alignment,
- jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
+ boolean scaleRightWrapped = true;
- if (globalColourScheme instanceof UserColourScheme)
- {
- globalColourScheme = UserDefinedColours.loadDefaultColours();
- ((UserColourScheme)globalColourScheme).setThreshold(0, getIgnoreGapsConsensus());
- }
+ boolean hasHiddenColumns = false;
- if (globalColourScheme != null)
- {
- globalColourScheme.setConsensus(hconsensus);
- }
- }
+ boolean hasHiddenRows = false;
- wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
- }
+ boolean showHiddenMarkers = true;
+ boolean cursorMode = false;
+ /**
+ * Keys are the feature types which are currently visible. Note: Values are
+ * not used!
+ */
+ Hashtable featuresDisplayed = null;
- /**
- * DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
- */
- public void setShowSequenceFeatures(boolean b)
- {
- showSequenceFeatures = b;
- }
+ /** DOCUMENT ME!! */
+ public Hashtable[] hconsensus;
- public boolean getShowSequenceFeatures()
- {
- return showSequenceFeatures;
- }
+ public Hashtable[] hStrucConsensus;
+ AlignmentAnnotation consensus;
+ AlignmentAnnotation strucConsensus;
- class ConservationThread extends Thread
- {
- AlignmentPanel ap;
- public ConservationThread(AlignmentPanel ap)
- {
- this.ap = ap;
- }
+ AlignmentAnnotation conservation;
- public void run()
- {
- try
- {
- updatingConservation = true;
+ AlignmentAnnotation quality;
- while (UPDATING_CONSERVATION)
- {
- try
- {
- if (ap != null)
- {
- ap.repaint();
- }
- Thread.sleep(200);
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
+ AlignmentAnnotation[] groupConsensus;
- UPDATING_CONSERVATION = true;
+ AlignmentAnnotation[] groupConservation;
+ boolean autoCalculateConsensus = true;
- int alWidth = alignment.getWidth();
- if(alWidth<0)
- return;
+ boolean autoCalculateStrucConsensus = true;
- Conservation cons = new jalview.analysis.Conservation("All",
- jalview.schemes.ResidueProperties.propHash, 3,
- alignment.getSequences(), 0, alWidth -1);
+ /** DOCUMENT ME!! */
+ public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
- cons.calculate();
- cons.verdict(false, ConsPercGaps);
+ // JBPNote Prolly only need this in the applet version.
+ private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
+ this);
- if (quality!=null)
- {
- cons.findQuality();
- }
+ boolean ignoreGapsInConsensusCalculation = false;
- String 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();
- }
+ boolean isDataset = false;
- for (int i = 0; i < alWidth; i++)
- {
- float value = 0;
-
- c = sequence.charAt(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()
- {
+ boolean antiAlias = false;
+ boolean padGaps = false;
- 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);
- }
- });
+ Rectangle explodedPosition;
- conservation = null;
- quality = null;
+ String viewName;
- System.out.println("Conservation calculation: " + error);
- System.gc();
+ String sequenceSetID;
- }
+ boolean gatherViewsHere = false;
- UPDATING_CONSERVATION = false;
- updatingConservation = false;
+ Stack historyList = new Stack();
- if(ap!=null)
- {
- ap.repaint();
- }
+ Stack redoList = new Stack();
- }
- }
+ Hashtable sequenceColours;
+ int thresholdTextColour = 0;
- ConservationThread conservationThread;
+ Color textColour = Color.black;
- ConsensusThread consensusThread;
+ Color textColour2 = Color.white;
- boolean consUpdateNeeded = false;
+ boolean rightAlignIds = false;
- static boolean UPDATING_CONSENSUS = false;
+ Hashtable hiddenRepSequences;
- static boolean UPDATING_CONSERVATION = false;
+ boolean sortByTree;
- boolean updatingConsensus = false;
+ /**
+ * Creates a new AlignViewport object.
+ *
+ * @param al
+ * alignment to view
+ */
+ public AlignViewport(AlignmentI al)
+ {
+ setAlignment(al);
+ init();
+ }
- boolean updatingConservation = false;
+ /**
+ * 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);
+ }
- /**
- * DOCUMENT ME!
- */
- public void updateConservation(final AlignmentPanel ap)
+ 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)
{
- if (alignment.isNucleotide() || conservation==null)
- return;
-
- conservationThread = new ConservationThread(ap);
- conservationThread.start();
+ Cache.log.debug("Setting viewport's sequence set id : "
+ + sequenceSetID);
}
-
- /**
- * DOCUMENT ME!
- */
- public void updateConsensus(final AlignmentPanel ap)
+ if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
{
- consensusThread = new ConsensusThread(ap);
- consensusThread.start();
+ Cache.log.debug("Setting viewport's view id : " + viewId);
}
+ setAlignment(al);
+ init();
+ }
-
- class ConsensusThread extends Thread
+ /**
+ * Create a new AlignViewport with hidden regions
+ *
+ * @param al
+ * AlignmentI
+ * @param hiddenColumns
+ * ColumnSelection
+ */
+ public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns)
+ {
+ setAlignment(al);
+ if (hiddenColumns != null)
{
- AlignmentPanel ap;
- public ConsensusThread(AlignmentPanel ap)
+ this.colSel = hiddenColumns;
+ if (hiddenColumns.getHiddenColumns() != null
+ && hiddenColumns.getHiddenColumns().size() > 0)
{
- this.ap = ap;
+ hasHiddenColumns = true;
}
- public void run()
+ else
{
- updatingConsensus = true;
- while (UPDATING_CONSENSUS)
- {
- try
- {
- if (ap != null)
- {
- ap.repaint();
- }
+ 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();
+ }
- Thread.sleep(200);
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
+ void init()
+ {
+ this.startRes = 0;
+ this.endRes = alignment.getWidth() - 1;
+ this.startSeq = 0;
+ this.endSeq = alignment.getHeight() - 1;
+ antiAlias = Cache.getDefault("ANTI_ALIAS", false);
- UPDATING_CONSENSUS = true;
+ showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
+ showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
- try
- {
- int aWidth = alignment.getWidth();
- if(aWidth<0)
- return;
+ rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
+ centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false);
+ autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
- consensus.annotations = null;
- consensus.annotations = new Annotation[aWidth];
+ 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 + "");
+ String fontSize = Cache.getDefault("FONT_SIZE", "10");
- hconsensus = new Hashtable[aWidth];
- AAFrequency.calculate(alignment.getSequencesArray(),
- 0,
- alignment.getWidth(),
- hconsensus);
+ seqNameItalics = Cache.getDefault("ID_ITALICS", true);
- 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);
- }
+ int style = 0;
+
+ if (fontStyle.equals("bold"))
+ {
+ style = 1;
+ }
+ else if (fontStyle.equals("italic"))
+ {
+ style = 2;
+ }
+
+ setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
+ alignment
+ .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
- if (globalColourScheme != null)
- globalColourScheme.setConsensus(hconsensus);
+ // We must set conservation and consensus before setting colour,
+ // as Blosum and Clustal require this to be done
+ if (hconsensus == null && !isDataset)
+ {
+ 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);
}
- catch (OutOfMemoryError error)
+
+ if (Cache.getDefault("SHOW_QUALITY", true))
{
- alignment.deleteAnnotation(consensus);
+ quality = new AlignmentAnnotation("Quality",
+ "Alignment Quality based on Blosum62 scores",
+ new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
+ quality.hasText = true;
+ quality.autoCalculated = true;
- 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();
+ alignment.addAnnotation(quality);
}
- UPDATING_CONSENSUS = false;
- updatingConsensus = false;
+ showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
+ false);
- if (ap != null)
{
- ap.repaint();
+
}
}
- }
- /**
- * 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);
+ 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);
+ 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);
}
}
- SequenceI sq = new Sequence("Consensus", seqs.toString());
- sq.setDescription("Percentage Identity Consensus "+((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
- return sq;
- }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public SequenceGroup getSelectionGroup()
- {
- return selectionGroup;
}
- /**
- * DOCUMENT ME!
- *
- * @param sg DOCUMENT ME!
- */
- public void setSelectionGroup(SequenceGroup sg)
+ if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
{
- selectionGroup = sg;
- }
+ globalColourScheme = ColourSchemeProperty.getColour(alignment,
+ jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getConservationSelected()
- {
- return conservationColourSelected;
- }
+ if (globalColourScheme instanceof UserColourScheme)
+ {
+ globalColourScheme = UserDefinedColours.loadDefaultColours();
+ ((UserColourScheme) globalColourScheme).setThreshold(0,
+ getIgnoreGapsConsensus());
+ }
- /**
- * DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
- */
- public void setConservationSelected(boolean b)
- {
- conservationColourSelected = b;
+ if (globalColourScheme != null)
+ {
+ globalColourScheme.setConsensus(hconsensus);
+ }
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getAbovePIDThreshold()
- {
- return abovePIDThreshold;
- }
+ 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!
- */
- public void setAbovePIDThreshold(boolean b)
+ /**
+ * set the flag
+ *
+ * @param b
+ * features are displayed if true
+ */
+ public void setShowSequenceFeatures(boolean b)
+ {
+ showSequenceFeatures = b;
+ }
+
+ public boolean getShowSequenceFeatures()
+ {
+ return showSequenceFeatures;
+ }
+
+ ConservationThread conservationThread;
+
+ ConsensusThread consensusThread;
+
+ 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;
+
+ /**
+ * centre columnar annotation labels in displayed alignment annotation TODO:
+ * add to jalviewXML and annotation display settings
+ */
+ boolean centreColumnLabels = false;
+
+ private boolean showdbrefs;
+
+ private boolean shownpfeats;
+
+ /**
+ * trigger update of conservation annotation
+ */
+ public void updateConservation(final AlignmentPanel ap)
+ {
+ // see note in mantis : issue number 8585
+ if (alignment.isNucleotide() || conservation == null
+ || !autoCalculateConsensus)
{
- abovePIDThreshold = b;
+ return;
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getStartRes()
+ conservationThread = new ConservationThread(this, ap);
+ conservationThread.start();
+ }
+
+ /**
+ * trigger update of consensus annotation
+ */
+ public void updateConsensus(final AlignmentPanel ap)
+ {
+ // see note in mantis : issue number 8585
+ if (consensus == null || !autoCalculateConsensus)
{
- return startRes;
+ return;
}
+ consensusThread = new ConsensusThread(ap);
+ consensusThread.start();
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getEndRes()
+ class ConsensusThread extends Thread
+ {
+ AlignmentPanel ap;
+
+ public ConsensusThread(AlignmentPanel ap)
{
- return endRes;
+ this.ap = ap;
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getStartSeq()
+ public void run()
{
- return startSeq;
+ updatingConsensus = true;
+ while (UPDATING_CONSENSUS)
+ {
+ try
+ {
+ if (ap != null)
+ {
+ ap.paintAlignment(false);
+ }
+
+ Thread.sleep(200);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ UPDATING_CONSENSUS = true;
+
+ try
+ {
+ int aWidth = (alignment != null) ? alignment.getWidth() : -1; // null
+ // pointer
+ // possibility
+ // here.
+ if (aWidth <= 0)
+ {
+ updatingConsensus = false;
+ UPDATING_CONSENSUS = false;
+ return;
+ }
+
+ consensus.annotations = null;
+ consensus.annotations = new Annotation[aWidth];
+
+ hconsensus = new Hashtable[aWidth];
+ AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment
+ .getWidth(), hconsensus, true);
+ updateAnnotation(true);
+ if (globalColourScheme != null)
+ {
+ globalColourScheme.setConsensus(hconsensus);
+ }
+
+ } catch (OutOfMemoryError error)
+ {
+ alignment.deleteAnnotation(consensus);
+
+ consensus = null;
+ hconsensus = null;
+ new OOMWarning("calculating consensus", error);
+ }
+ UPDATING_CONSENSUS = false;
+ updatingConsensus = false;
+
+ if (ap != null)
+ {
+ ap.paintAlignment(true);
+ }
}
/**
- * DOCUMENT ME!
- *
- * @param cs DOCUMENT ME!
+ * update the consensus annotation from the sequence profile data using
+ * current visualization settings.
*/
- public void setGlobalColourScheme(ColourSchemeI cs)
+ public void updateAnnotation()
{
- globalColourScheme = cs;
+ updateAnnotation(false);
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public ColourSchemeI getGlobalColourScheme()
+ protected void updateAnnotation(boolean immediate)
{
- return globalColourScheme;
+ // 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);
+ }
}
+ }
- /**
- * DOCUMENT ME!
- *
- * @param res DOCUMENT ME!
- */
- public void setStartRes(int res)
+ // --------START Structure Conservation
+ public void updateStrucConsensus(final AlignmentPanel ap)
+ {
+ // see note in mantis : issue number 8585
+ if (strucConsensus == null || !autoCalculateStrucConsensus)
{
- this.startRes = res;
+ return;
}
+ strucConsensusThread = new StrucConsensusThread(ap);
+ strucConsensusThread.start();
+ }
- /**
- * DOCUMENT ME!
- *
- * @param seq DOCUMENT ME!
- */
- public void setStartSeq(int seq)
+ class StrucConsensusThread extends Thread
+ {
+ AlignmentPanel ap;
+
+ public StrucConsensusThread(AlignmentPanel ap)
{
- this.startSeq = seq;
+ this.ap = ap;
}
- /**
- * DOCUMENT ME!
- *
- * @param res DOCUMENT ME!
- */
- public void setEndRes(int res)
+ public void run()
{
- if (res > (alignment.getWidth() - 1))
+ updatingStrucConsensus = true;
+ while (UPDATING_STRUC_CONSENSUS)
+ {
+ try
+ {
+ if (ap != null)
+ {
+ ap.paintAlignment(false);
+ }
+
+ Thread.sleep(200);
+ } catch (Exception ex)
{
- // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
- res = alignment.getWidth() - 1;
+ ex.printStackTrace();
}
+ }
+
+ UPDATING_STRUC_CONSENSUS = true;
- if (res < 0)
+ try
+ {
+ int aWidth = (alignment != null) ? alignment.getWidth() : -1; // null
+ // pointer
+ // possibility
+ // here.
+ if (aWidth <= 0)
{
- res = 0;
+ updatingStrucConsensus = false;
+ UPDATING_STRUC_CONSENSUS = false;
+ return;
}
- this.endRes = res;
- }
+ strucConsensus.annotations = null;
+ strucConsensus.annotations = new Annotation[aWidth];
- /**
- * DOCUMENT ME!
- *
- * @param seq DOCUMENT ME!
- */
- public void setEndSeq(int seq)
- {
- if (seq > alignment.getHeight())
+ hStrucConsensus = new Hashtable[aWidth];
+
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
+ AlignmentAnnotation rnaStruc = null;
+ for (int i = 0; i < aa.length; i++)
{
- seq = alignment.getHeight();
+ if (aa[i].getRNAStruc() != null)
+ {
+ rnaStruc = aa[i];
+ break;
+ }
}
- if (seq < 0)
+ 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)
{
- seq = 0;
+ globalColourScheme.setConsensus(hStrucConsensus);
}
- this.endSeq = seq;
+ } 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);
+ }
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * update the consensus annotation from the sequence profile data using
+ * current visualization settings.
*/
- public int getEndSeq()
+ public void updateAnnotation()
{
- return endSeq;
+ updateAnnotation(false);
}
- /**
- * DOCUMENT ME!
- *
- * @param f DOCUMENT ME!
- */
- public void setFont(Font f)
+ protected void updateAnnotation(boolean immediate)
{
- font = f;
-
- Container c = new Container();
-
- java.awt.FontMetrics fm = c.getFontMetrics(font);
- setCharHeight(fm.getHeight());
- setCharWidth(fm.charWidth('M'));
- validCharWidth = true;
+ // 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);
+ }
}
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Font getFont()
+ // --------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)
{
- return font;
+ updateConsensus(null);
}
-
- /**
- * DOCUMENT ME!
- *
- * @param w DOCUMENT ME!
- */
- public void setCharWidth(int w)
+ if (consensus == null)
{
- this.charWidth = w;
+ return null;
}
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getCharWidth()
+ StringBuffer seqs = new StringBuffer();
+ for (int i = 0; i < consensus.annotations.length; i++)
{
- return charWidth;
+ 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);
+ }
+ }
}
- /**
- * DOCUMENT ME!
- *
- * @param h DOCUMENT ME!
- */
- public void setCharHeight(int h)
+ 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;
+ }
+
+ /**
+ * Set the selection group for this window.
+ *
+ * @param sg
+ * - group holding references to sequences in this alignment view
+ *
+ */
+ public void setSelectionGroup(SequenceGroup sg)
+ {
+ selectionGroup = sg;
+ }
+
+ /**
+ * GUI state
+ *
+ * @return true if conservation based shading is enabled
+ */
+ public boolean getConservationSelected()
+ {
+ return conservationColourSelected;
+ }
+
+ /**
+ * GUI state
+ *
+ * @param b
+ * enable conservation based shading
+ */
+ public void setConservationSelected(boolean b)
+ {
+ conservationColourSelected = b;
+ }
+
+ /**
+ * GUI state
+ *
+ * @return true if percent identity threshold is applied to shading
+ */
+ public boolean getAbovePIDThreshold()
+ {
+ return abovePIDThreshold;
+ }
+
+ /**
+ * GUI state
+ *
+ *
+ * @param b
+ * indicate if percent identity threshold is applied to shading
+ */
+ public void setAbovePIDThreshold(boolean b)
+ {
+ abovePIDThreshold = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getStartRes()
+ {
+ 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 < 0)
+ {
+ seq = 0;
+ }
+
+ this.endSeq = seq;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getEndSeq()
+ {
+ return endSeq;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param f
+ * DOCUMENT ME!
+ */
+ public void setFont(Font f)
+ {
+ font = f;
+
+ Container c = new Container();
+
+ java.awt.FontMetrics fm = c.getFontMetrics(font);
+ setCharHeight(fm.getHeight());
+ setCharWidth(fm.charWidth('M'));
+ validCharWidth = true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Font getFont()
+ {
+ return font;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param w
+ * DOCUMENT ME!
+ */
+ public void setCharWidth(int w)
+ {
+ this.charWidth = w;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getCharWidth()
+ {
+ return charWidth;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param h
+ * DOCUMENT ME!
+ */
+ public void setCharHeight(int h)
+ {
+ this.charHeight = h;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getCharHeight()
+ {
+ return charHeight;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param w
+ * DOCUMENT ME!
+ */
+ public void setWrappedWidth(int w)
+ {
+ this.wrappedWidth = w;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getWrappedWidth()
+ {
+ return wrappedWidth;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public AlignmentI getAlignment()
+ {
+ return alignment;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param align
+ * DOCUMENT ME!
+ */
+ public void setAlignment(AlignmentI align)
+ {
+ if (alignment != null && alignment.getCodonFrames() != null)
+ {
+ StructureSelectionManager.getStructureSelectionManager(
+ Desktop.instance).removeMappings(alignment.getCodonFrames());
+ }
+ this.alignment = align;
+ if (alignment.getCodonFrames() != null)
+ {
+ StructureSelectionManager.getStructureSelectionManager(
+ Desktop.instance).addMappings(alignment.getCodonFrames());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
+ */
+ public void setWrapAlignment(boolean state)
+ {
+ wrapAlignment = state;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
+ */
+ public void setShowText(boolean state)
+ {
+ showText = state;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
+ */
+ public void setRenderGaps(boolean state)
+ {
+ renderGaps = state;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getColourText()
+ {
+ return showColourText;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
+ */
+ public void setColourText(boolean state)
+ {
+ showColourText = state;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
+ */
+ public void setShowBoxes(boolean state)
+ {
+ showBoxes = state;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getWrapAlignment()
+ {
+ return wrapAlignment;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getShowText()
+ {
+ return showText;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getShowBoxes()
+ {
+ return showBoxes;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public char getGapCharacter()
+ {
+ return getAlignment().getGapCharacter();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param gap
+ * DOCUMENT ME!
+ */
+ public void setGapCharacter(char gap)
+ {
+ if (getAlignment() != null)
+ {
+ getAlignment().setGapCharacter(gap);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param thresh
+ * DOCUMENT ME!
+ */
+ public void setThreshold(int thresh)
+ {
+ threshold = thresh;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getThreshold()
+ {
+ return threshold;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param inc
+ * DOCUMENT ME!
+ */
+ public void setIncrement(int inc)
+ {
+ increment = inc;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getIncrement()
+ {
+ return increment;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public ColumnSelection getColumnSelection()
+ {
+ return colSel;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param tree
+ * DOCUMENT ME!
+ */
+ public void setCurrentTree(NJTree tree)
+ {
+ currentTree = tree;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public NJTree getCurrentTree()
+ {
+ return currentTree;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
+ */
+ public void setColourAppliesToAllGroups(boolean b)
+ {
+ colourAppliesToAllGroups = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getColourAppliesToAllGroups()
+ {
+ return colourAppliesToAllGroups;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getShowJVSuffix()
+ {
+ return showJVSuffix;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
+ */
+ public void setShowJVSuffix(boolean b)
+ {
+ showJVSuffix = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getShowAnnotation()
+ {
+ return showAnnotation;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
+ */
+ public void setShowAnnotation(boolean b)
+ {
+ showAnnotation = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getScaleAboveWrapped()
+ {
+ return scaleAboveWrapped;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getScaleLeftWrapped()
+ {
+ return scaleLeftWrapped;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getScaleRightWrapped()
+ {
+ return scaleRightWrapped;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
+ */
+ public void setScaleAboveWrapped(boolean b)
+ {
+ scaleAboveWrapped = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
+ */
+ public void setScaleLeftWrapped(boolean b)
+ {
+ scaleLeftWrapped = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
+ */
+ public void setScaleRightWrapped(boolean b)
+ {
+ scaleRightWrapped = b;
+ }
+
+ /**
+ * Property change listener for changes in alignment
+ *
+ * @param listener
+ * DOCUMENT ME!
+ */
+ public void addPropertyChangeListener(
+ java.beans.PropertyChangeListener listener)
+ {
+ changeSupport.addPropertyChangeListener(listener);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param listener
+ * DOCUMENT ME!
+ */
+ public void removePropertyChangeListener(
+ java.beans.PropertyChangeListener listener)
+ {
+ changeSupport.removePropertyChangeListener(listener);
+ }
+
+ /**
+ * Property change listener for changes in alignment
+ *
+ * @param prop
+ * DOCUMENT ME!
+ * @param oldvalue
+ * DOCUMENT ME!
+ * @param newvalue
+ * DOCUMENT ME!
+ */
+ public void firePropertyChange(String prop, Object oldvalue,
+ Object newvalue)
+ {
+ changeSupport.firePropertyChange(prop, oldvalue, newvalue);
+ }
+
+ public void setIgnoreGapsConsensus(boolean b, AlignmentPanel ap)
+ {
+ ignoreGapsInConsensusCalculation = b;
+ updateConsensus(ap);
+ if (globalColourScheme != null)
+ {
+ globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
+ ignoreGapsInConsensusCalculation);
+ }
+ }
+
+ public boolean getIgnoreGapsConsensus()
+ {
+ return ignoreGapsInConsensusCalculation;
+ }
+
+ public void setDataset(boolean b)
+ {
+ isDataset = b;
+ }
+
+ public boolean isDataset()
+ {
+ return isDataset;
+ }
+
+ public void hideSelectedColumns()
+ {
+ if (colSel.size() < 1)
+ {
+ return;
+ }
+
+ colSel.hideSelectedColumns();
+ setSelectionGroup(null);
+
+ hasHiddenColumns = true;
+ }
+
+ public void hideColumns(int start, int end)
+ {
+ if (start == end)
+ {
+ colSel.hideColumns(start);
+ }
+ else
+ {
+ colSel.hideColumns(start, end);
+ }
+
+ hasHiddenColumns = true;
+ }
+
+ public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
+ {
+ int sSize = sg.getSize();
+ if (sSize < 2)
{
- this.charHeight = h;
+ return;
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getCharHeight()
+ if (hiddenRepSequences == null)
{
- return charHeight;
+ hiddenRepSequences = new Hashtable();
}
- /**
- * DOCUMENT ME!
- *
- * @param w DOCUMENT ME!
- */
- public void setWrappedWidth(int w)
+ 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++)
{
- this.wrappedWidth = w;
+ if (sg.getSequenceAt(i) != repSequence)
+ {
+ if (index == sSize - 1)
+ {
+ return;
+ }
+
+ seqs[index++] = sg.getSequenceAt(i);
+ }
}
+ sg.setSeqrep(repSequence);
+ sg.setHidereps(true);
+ hideSequence(seqs);
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getWrappedWidth()
+ }
+
+ public void hideAllSelectedSeqs()
+ {
+ if (selectionGroup == null || selectionGroup.getSize() < 1)
{
- return wrappedWidth;
+ return;
}
+ SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public AlignmentI getAlignment()
- {
- return alignment;
- }
+ hideSequence(seqs);
- /**
- * DOCUMENT ME!
- *
- * @param align DOCUMENT ME!
- */
- public void setAlignment(AlignmentI align)
- {
- this.alignment = align;
- }
+ setSelectionGroup(null);
+ }
- /**
- * DOCUMENT ME!
- *
- * @param state DOCUMENT ME!
- */
- public void setWrapAlignment(boolean state)
+ public void hideSequence(SequenceI[] seq)
+ {
+ if (seq != null)
{
- wrapAlignment = state;
+ for (int i = 0; i < seq.length; i++)
+ {
+ alignment.getHiddenSequences().hideSequence(seq[i]);
+ }
+ hasHiddenRows = true;
+ firePropertyChange("alignment", null, alignment.getSequences());
}
+ }
- /**
- * DOCUMENT ME!
- *
- * @param state DOCUMENT ME!
- */
- public void setShowText(boolean state)
+ public void showSequence(int index)
+ {
+ Vector tmp = alignment.getHiddenSequences().showSequence(index,
+ hiddenRepSequences);
+ if (tmp.size() > 0)
{
- showText = state;
- }
+ if (selectionGroup == null)
+ {
+ selectionGroup = new SequenceGroup();
+ selectionGroup.setEndRes(alignment.getWidth() - 1);
+ }
- /**
- * DOCUMENT ME!
- *
- * @param state DOCUMENT ME!
- */
- public void setRenderGaps(boolean state)
- {
- renderGaps = state;
+ for (int t = 0; t < tmp.size(); t++)
+ {
+ selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
+ }
+ firePropertyChange("alignment", null, alignment.getSequences());
+ sendSelection();
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getColourText()
+ if (alignment.getHiddenSequences().getSize() < 1)
{
- return showColourText;
+ hasHiddenRows = false;
}
+ }
- /**
- * DOCUMENT ME!
- *
- * @param state DOCUMENT ME!
- */
- public void setColourText(boolean state)
+ public void showColumn(int col)
+ {
+ colSel.revealHiddenColumns(col);
+ if (colSel.getHiddenColumns() == null)
{
- showColourText = state;
+ hasHiddenColumns = false;
}
+ }
- /**
- * DOCUMENT ME!
- *
- * @param state DOCUMENT ME!
- */
- public void setShowBoxes(boolean state)
- {
- showBoxes = state;
- }
+ public void showAllHiddenColumns()
+ {
+ colSel.revealAllHiddenColumns();
+ hasHiddenColumns = false;
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getWrapAlignment()
+ public void showAllHiddenSeqs()
+ {
+ if (alignment.getHiddenSequences().getSize() > 0)
{
- return wrapAlignment;
+ if (selectionGroup == null)
+ {
+ selectionGroup = new SequenceGroup();
+ selectionGroup.setEndRes(alignment.getWidth() - 1);
+ }
+ Vector tmp = alignment.getHiddenSequences().showAll(
+ hiddenRepSequences);
+ for (int t = 0; t < tmp.size(); t++)
+ {
+ selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
+ }
+ firePropertyChange("alignment", null, alignment.getSequences());
+ sendSelection();
+ hasHiddenRows = false;
+ hiddenRepSequences = null;
+ }
+ }
+
+ public void invertColumnSelection()
+ {
+ colSel.invertColumnSelection(0, alignment.getWidth());
+ }
+
+ public int adjustForHiddenSeqs(int alignmentIndex)
+ {
+ return alignment.getHiddenSequences().adjustForHiddenSeqs(
+ alignmentIndex);
+ }
+
+ /**
+ * This method returns an array of new SequenceI objects derived from the
+ * whole alignment or just the current selection with start and end points
+ * adjusted
+ *
+ * @note if you need references to the actual SequenceI objects in the
+ * alignment or currently selected then use getSequenceSelection()
+ * @return selection as new sequenceI objects
+ */
+ public SequenceI[] getSelectionAsNewSequence()
+ {
+ SequenceI[] sequences;
+
+ if (selectionGroup == null)
+ {
+ sequences = alignment.getSequencesArray();
+ AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
+ for (int i = 0; i < sequences.length; i++)
+ {
+ sequences[i] = new Sequence(sequences[i], annots); // construct new
+ // sequence with
+ // subset of visible
+ // annotation
+ }
}
+ else
+ {
+ sequences = selectionGroup.getSelectionAsNewSequences(alignment);
+ }
+
+ return sequences;
+ }
+
+ /**
+ * get the currently selected sequence objects or all the sequences in the
+ * alignment.
+ *
+ * @return array of references to sequence objects
+ */
+ public SequenceI[] getSequenceSelection()
+ {
+ SequenceI[] sequences = null;
+ if (selectionGroup != null)
+ {
+ sequences = selectionGroup.getSequencesInOrder(alignment);
+ }
+ if (sequences == null)
+ {
+ sequences = alignment.getSequencesArray();
+ }
+ return sequences;
+ }
+
+ /**
+ * This method returns the visible alignment as text, as seen on the GUI, ie
+ * if columns are hidden they will not be returned in the result. Use this for
+ * calculating trees, PCA, redundancy etc on views which contain hidden
+ * columns.
+ *
+ * @return String[]
+ */
+ public jalview.datamodel.CigarArray getViewAsCigars(
+ boolean selectedRegionOnly)
+ {
+ return new jalview.datamodel.CigarArray(alignment,
+ (hasHiddenColumns ? colSel : null),
+ (selectedRegionOnly ? selectionGroup : null));
+ }
+
+ /**
+ * return a compact representation of the current alignment selection to pass
+ * to an analysis function
+ *
+ * @param selectedOnly
+ * boolean true to just return the selected view
+ * @return AlignmentView
+ */
+ public jalview.datamodel.AlignmentView getAlignmentView(
+ boolean selectedOnly)
+ {
+ return getAlignmentView(selectedOnly, false);
+ }
+
+ /**
+ * return a compact representation of the current alignment selection to pass
+ * to an analysis function
+ *
+ * @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
+ */
+ public jalview.datamodel.AlignmentView getAlignmentView(
+ boolean selectedOnly, boolean markGroups)
+ {
+ 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.
+ *
+ * @return String[]
+ */
+ public String[] getViewAsString(boolean selectedRegionOnly)
+ {
+ String[] selection = null;
+ SequenceI[] seqs = null;
+ int i, iSize;
+ int start = 0, end = 0;
+ if (selectedRegionOnly && selectionGroup != null)
+ {
+ iSize = selectionGroup.getSize();
+ seqs = selectionGroup.getSequencesInOrder(alignment);
+ start = selectionGroup.getStartRes();
+ end = selectionGroup.getEndRes() + 1;
+ }
+ else
+ {
+ iSize = alignment.getHeight();
+ seqs = alignment.getSequencesArray();
+ end = alignment.getWidth();
+ }
+
+ selection = new String[iSize];
+ if (hasHiddenColumns)
+ {
+ selection = colSel.getVisibleSequenceStrings(start, end, seqs);
+ }
+ else
+ {
+ for (i = 0; i < iSize; i++)
+ {
+ selection[i] = seqs[i].getSequenceAsString(start, end);
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getShowText()
- {
- return showText;
}
+ return selection;
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getShowBoxes()
- {
- return showBoxes;
- }
+ public int[][] getVisibleRegionBoundaries(int min, int max)
+ {
+ Vector regions = new Vector();
+ int start = min;
+ int end = max;
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public char getGapCharacter()
+ do
{
- return getAlignment().getGapCharacter();
- }
+ if (hasHiddenColumns)
+ {
+ if (start == 0)
+ {
+ start = colSel.adjustForHiddenColumns(start);
+ }
- /**
- * DOCUMENT ME!
- *
- * @param gap DOCUMENT ME!
- */
- public void setGapCharacter(char gap)
- {
- if (getAlignment() != null)
+ end = colSel.getHiddenBoundaryRight(start);
+ if (start == end)
{
- getAlignment().setGapCharacter(gap);
+ end = max;
}
- }
+ if (end > max)
+ {
+ end = max;
+ }
+ }
- /**
- * DOCUMENT ME!
- *
- * @param thresh DOCUMENT ME!
- */
- public void setThreshold(int thresh)
- {
- threshold = thresh;
- }
+ regions.addElement(new int[]
+ { start, end });
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getThreshold()
- {
- return threshold;
- }
+ if (hasHiddenColumns)
+ {
+ start = colSel.adjustForHiddenColumns(end);
+ start = colSel.getHiddenBoundaryLeft(start) + 1;
+ }
+ } while (end < max);
- /**
- * DOCUMENT ME!
- *
- * @param inc DOCUMENT ME!
- */
- public void setIncrement(int inc)
- {
- increment = inc;
- }
+ int[][] startEnd = new int[regions.size()][2];
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getIncrement()
- {
- return increment;
- }
+ regions.copyInto(startEnd);
+ return startEnd;
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public ColumnSelection getColumnSelection()
- {
- return colSel;
- }
+ }
+ public boolean getShowHiddenMarkers()
+ {
+ return showHiddenMarkers;
+ }
- /**
- * DOCUMENT ME!
- *
- * @param tree DOCUMENT ME!
- */
- public void setCurrentTree(NJTree tree)
- {
- currentTree = tree;
- }
+ public void setShowHiddenMarkers(boolean show)
+ {
+ showHiddenMarkers = show;
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public NJTree getCurrentTree()
+ public String getSequenceSetId()
+ {
+ if (sequenceSetID == null)
{
- return currentTree;
+ sequenceSetID = alignment.hashCode() + "";
}
- /**
- * DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
- */
- public void setColourAppliesToAllGroups(boolean b)
- {
- colourAppliesToAllGroups = b;
- }
+ return sequenceSetID;
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getColourAppliesToAllGroups()
- {
- return colourAppliesToAllGroups;
- }
+ /**
+ * unique viewId for synchronizing state with stored Jalview Project
+ *
+ */
+ private String viewId = null;
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getShowJVSuffix()
+ public String getViewId()
+ {
+ if (viewId == null)
{
- return showJVSuffix;
+ viewId = this.getSequenceSetId() + "." + this.hashCode() + "";
}
+ return viewId;
+ }
- /**
- * DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
- */
- public void setShowJVSuffix(boolean b)
+ public void alignmentChanged(AlignmentPanel ap)
+ {
+ if (padGaps)
{
- showJVSuffix = b;
+ alignment.padGaps();
}
-
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getShowAnnotation()
+ if (hconsensus != null && autoCalculateConsensus)
{
- return showAnnotation;
+ updateConservation(ap);
}
-
- /**
- * DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
- */
- public void setShowAnnotation(boolean b)
+ if (autoCalculateConsensus)
{
- showAnnotation = b;
+ updateConsensus(ap);
}
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getScaleAboveWrapped()
+ if (autoCalculateStrucConsensus)
{
- return scaleAboveWrapped;
+ updateStrucConsensus(ap);
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getScaleLeftWrapped()
+ // Reset endRes of groups if beyond alignment width
+ int alWidth = alignment.getWidth();
+ Vector groups = alignment.getGroups();
+ if (groups != null)
{
- return scaleLeftWrapped;
+ for (int i = 0; i < groups.size(); i++)
+ {
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+ if (sg.getEndRes() > alWidth)
+ {
+ sg.setEndRes(alWidth - 1);
+ }
+ }
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getScaleRightWrapped()
+ if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)
{
- return scaleRightWrapped;
+ selectionGroup.setEndRes(alWidth - 1);
}
- /**
- * DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
- */
- public void setScaleAboveWrapped(boolean b)
- {
- scaleAboveWrapped = b;
- }
+ resetAllColourSchemes();
- /**
- * DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
- */
- public void setScaleLeftWrapped(boolean b)
- {
- scaleLeftWrapped = b;
- }
+ // alignment.adjustSequenceAnnotations();
+ }
- /**
- * DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
- */
- public void setScaleRightWrapped(boolean b)
+ void resetAllColourSchemes()
+ {
+ ColourSchemeI cs = globalColourScheme;
+ if (cs != null)
{
- scaleRightWrapped = b;
+ 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);
+ }
}
- /**
- * Property change listener for changes in alignment
- *
- * @param listener DOCUMENT ME!
- */
- public void addPropertyChangeListener(
- java.beans.PropertyChangeListener listener)
+ int s, sSize = alignment.getGroups().size();
+ for (s = 0; s < sSize; s++)
{
- changeSupport.addPropertyChangeListener(listener);
+ 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();
}
+ }
- /**
- * DOCUMENT ME!
- *
- * @param listener DOCUMENT ME!
- */
- public void removePropertyChangeListener(
- java.beans.PropertyChangeListener listener)
+ public Color getSequenceColour(SequenceI seq)
+ {
+ if (sequenceColours == null || !sequenceColours.containsKey(seq))
{
- changeSupport.removePropertyChangeListener(listener);
+ return Color.white;
}
-
- /**
- * 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)
+ else
{
- changeSupport.firePropertyChange(prop, oldvalue, newvalue);
+ return (Color) sequenceColours.get(seq);
}
+ }
- public void setIgnoreGapsConsensus(boolean b, AlignmentPanel ap)
+ public void setSequenceColour(SequenceI seq, Color col)
+ {
+ if (sequenceColours == null)
{
- ignoreGapsInConsensusCalculation = b;
- updateConsensus(ap);
- if(globalColourScheme!=null)
- {
- globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation);
- }
+ sequenceColours = new Hashtable();
}
- public boolean getIgnoreGapsConsensus()
+ if (col == null)
{
- return ignoreGapsInConsensusCalculation;
+ sequenceColours.remove(seq);
}
-
- public void setDataset(boolean b)
+ else
{
- isDataset = b;
+ sequenceColours.put(seq, col);
}
+ }
- public boolean isDataset()
+ /**
+ * 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)
{
- return isDataset;
+ start = selectionGroup.getStartRes();
+ end = selectionGroup.getEndRes() + 1;
}
-
-
- public void hideSelectedColumns()
+ else
{
- if (colSel.size() < 1)
- return;
-
- colSel.hideSelectedColumns();
- setSelectionGroup(null);
-
- hasHiddenColumns = true;
+ 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() };
+ }
- public void hideColumns(int start, int end)
+ /**
+ * 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)
{
- if(start==end)
- colSel.hideColumns(start);
- else
- colSel.hideColumns(start, end);
-
- hasHiddenColumns = true;
+ return true;
}
-
- public void hideAllSelectedSeqs()
+ long[] cstate = getUndoRedoHash();
+ if (cstate.length != undoredo.length)
{
- if (selectionGroup == null)
- return;
-
- SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
-
- hideSequence(seqs);
-
- setSelectionGroup(null);
+ return true;
}
- public void hideSequence(SequenceI [] seq)
+ for (int i = 0; i < cstate.length; i++)
{
- if(seq!=null)
+ if (cstate[i] != undoredo[i])
{
- for (int i = 0; i < seq.length; i++)
- alignment.getHiddenSequences().hideSequence(seq[i]);
-
- hasHiddenRows = true;
- firePropertyChange("alignment", null, alignment.getSequences());
+ return true;
}
}
+ return false;
+ }
- public void showSequence(int index)
- {
- Vector tmp = alignment.getHiddenSequences().showSequence(index);
- 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());
- }
+ public boolean getCentreColumnLabels()
+ {
+ return centreColumnLabels;
+ }
- if(alignment.getHiddenSequences().getSize()<1)
- hasHiddenRows = false;
- }
+ public void setCentreColumnLabels(boolean centrecolumnlabels)
+ {
+ centreColumnLabels = centrecolumnlabels;
+ }
- public void showColumn(int col)
+ public void updateSequenceIdColours()
+ {
+ Vector groups = alignment.getGroups();
+ if (sequenceColours == null)
{
- colSel.revealHiddenColumns(col);
- if(colSel.getHiddenColumns()==null)
- hasHiddenColumns = false;
+ sequenceColours = new Hashtable();
}
-
- public void showAllHiddenColumns()
+ for (int ig = 0, igSize = groups.size(); ig < igSize; ig++)
{
- colSel.revealAllHiddenColumns();
- hasHiddenColumns = false;
- }
-
- public void showAllHiddenSeqs()
- {
- if(alignment.getHiddenSequences().getSize()>0)
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(ig);
+ if (sg.idColour != null)
{
- if(selectionGroup==null)
+ Vector sqs = sg.getSequences(hiddenRepSequences);
+ for (int s = 0, sSize = sqs.size(); s < sSize; s++)
{
- selectionGroup = new SequenceGroup();
- selectionGroup.setEndRes(alignment.getWidth()-1);
+ sequenceColours.put(sqs.elementAt(s), sg.idColour);
}
- Vector tmp = alignment.getHiddenSequences().showAll();
- for(int t=0; t<tmp.size(); t++)
- {
- selectionGroup.addSequence(
- (SequenceI)tmp.elementAt(t), false
- );
- }
- firePropertyChange("alignment", null, alignment.getSequences());
- hasHiddenRows = false;
}
}
-
- public void invertColumnSelection()
- {
- int column;
- for(int i=0; i<alignment.getWidth(); i++)
+ }
+
+ /**
+ * 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)
{
- column = i;
-
- if(colSel.contains(column))
- colSel.removeElement(column);
- else
- colSel.addElement(column);
-
+ sgrouphash = hc;
}
-
- }
-
- public int adjustForHiddenSeqs(int 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[]
- */
- public SequenceI[] getSelectionAsNewSequence()
- {
- SequenceI[] sequences;
-
- if (selectionGroup == null)
- sequences = alignment.getSequencesArray();
- else
- sequences = selectionGroup.getSelectionAsNewSequences(alignment);
-
- return sequences;
- }
-
- /**
- * This method returns the visible alignment as text, as
- * seen on the GUI, ie if columns are hidden they will not
- * be returned in the result.
- * Use this for calculating trees, PCA, redundancy etc on views
- * which contain hidden columns.
- * @return String[]
- */
- public jalview.datamodel.CigarArray getViewAsCigars(boolean selectedRegionOnly)
- {
- CigarArray selection=null;
- SequenceI [] seqs= null;
- int i, iSize;
- int start = 0, end = 0;
- if(selectedRegionOnly && selectionGroup!=null)
+ 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)
{
- iSize = selectionGroup.getSize(false);
- seqs = selectionGroup.getSequencesInOrder(alignment);
- start = selectionGroup.getStartRes();
- end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
+ colselhash = hc;
}
- else
+ 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)
{
- iSize = alignment.getHeight();
- seqs = alignment.getSequencesArray();
- end = alignment.getWidth()-1;
+ return aps[p];
}
- SeqCigar[] selseqs = new SeqCigar[iSize];
- for(i=0; i<iSize; i++)
+ }
+ 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)
{
- 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;
- }
-
- if (hideStart>end)
- break;
-
- if (hideEnd>end)
- hideEnd=end;
-
- 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);
+ consensusThread.updateAnnotation();
}
- 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
- */
- jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly) {
- // 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);
+ if (strucConsensusThread != null)
+ {
+ strucConsensusThread.updateAnnotation();
}
- return null;
}
- /**
- * 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)
- {
- String [] selection = null;
- SequenceI [] seqs= null;
- int i, iSize;
- int start = 0, end = 0;
- if(selectedRegionOnly && selectionGroup!=null)
+ 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))
{
- iSize = selectionGroup.getSize(false);
- seqs = selectionGroup.getSequencesInOrder(alignment);
- start = selectionGroup.getStartRes();
- end = selectionGroup.getEndRes()+1;
+ // do nothing
+ return;
}
- else
+ if (colSel == null)
{
- iSize = alignment.getHeight();
- seqs = alignment.getSequencesArray();
- end = alignment.getWidth();
+ colSel = new ColumnSelection();
}
-
- selection = new String[iSize];
- if (hasHiddenColumns) {
- selection = colSel.getVisibleSequenceStrings(start, end, seqs);
- } else {
- for(i=0; i<iSize; i++)
- {
- selection[i] = seqs[i].getSequence(start, end);
- }
-
+ for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
+ {
+ colSel.addElement(cspos);
}
- return selection;
- }
-
- public boolean getShowHiddenMarkers()
- {
- return showHiddenMarkers;
- }
-
- public void setShowHiddenMarkers(boolean show)
- {
- showHiddenMarkers = show;
}
-
- public String getSequenceSetId()
- {
- if(sequenceSetID==null)
- sequenceSetID = alignment.hashCode()+"";
-
- return sequenceSetID;
- }
-
- public void alignmentChanged(AlignmentPanel ap)
- {
- if (padGaps)
- alignment.padGaps();
-
- if (hconsensus != null && autoCalculateConsensus)
- {
- updateConsensus(ap);
- updateConservation(ap);
- }
-
- //Reset endRes of groups if beyond alignment width
- int alWidth = alignment.getWidth();
- Vector groups = alignment.getGroups();
- if(groups!=null)
- {
- for(int i=0; i<groups.size(); i++)
- {
- SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
- if(sg.getEndRes()>alWidth)
- sg.setEndRes(alWidth-1);
- }
- }
-
- if(selectionGroup!=null && selectionGroup.getEndRes()>alWidth)
- selectionGroup.setEndRes(alWidth-1);
-
- resetAllColourSchemes();
-
- alignment.adjustSequenceAnnotations();
- }
-
-
- void resetAllColourSchemes()
- {
- ColourSchemeI cs = globalColourScheme;
- if(cs!=null)
+ }
+
+ 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<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
+ for (PDBEntry pdb : pdbEntries)
+ {
+ ArrayList<SequenceI> seqs = new ArrayList<SequenceI>();
+ for (int i = 0; i < alignment.getHeight(); i++)
{
- if (cs instanceof ClustalxColourScheme)
+ Vector pdbs = alignment.getSequenceAt(i).getDatasetSequence()
+ .getPDBId();
+ if (pdbs == null)
+ continue;
+ SequenceI sq;
+ for (int p = 0; p < pdbs.size(); p++)
{
- ( (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);
- }
- }
+ PDBEntry p1 = (PDBEntry) pdbs.elementAt(p);
+ if (p1.getId().equals(pdb.getId()))
+ {
+ if (!seqs.contains(sq = alignment.getSequenceAt(i)))
+ seqs.add(sq);
- int s, sSize = alignment.getGroups().size();
- for(s=0; s<sSize; s++)
- {
- SequenceGroup sg = (SequenceGroup)alignment.getGroups().elementAt(s);
- if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
- {
- ((ClustalxColourScheme)sg.cs).resetClustalX(
- sg.getSequences(true), sg.getWidth());
+ continue;
+ }
}
- sg.recalcConservation();
}
+ seqvectors.add(seqs.toArray(new SequenceI[seqs.size()]));
}
-
-
- public Color getSequenceColour(SequenceI seq)
- {
- if(sequenceColours==null || !sequenceColours.containsKey(seq))
- return Color.white;
- else
- return (Color)sequenceColours.get(seq);
- }
-
- public void setSequenceColour(SequenceI seq, Color col)
- {
- if(sequenceColours==null)
- sequenceColours = new Hashtable();
-
- if(col == null)
- sequenceColours.remove(seq);
- else
- sequenceColours.put(seq, col);
- }
-
-
+ return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
+ }
}
git://source.jalview.org / jalview.git / blobdiff