/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
import java.awt.*;
import jalview.analysis.*;
+
import jalview.bin.*;
+
import jalview.datamodel.*;
+
import jalview.schemes.*;
+import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
-public class AlignViewport
+public class AlignViewport implements SelectionSource
{
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;
/** DOCUMENT ME!! */
public Hashtable[] hconsensus;
+
AlignmentAnnotation consensus;
+
AlignmentAnnotation conservation;
+
AlignmentAnnotation quality;
+
boolean autoCalculateConsensus = true;
/** DOCUMENT ME!! */
public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
// JBPNote Prolly only need this in the applet version.
- private java.beans.PropertyChangeSupport changeSupport = new java.beans.
- PropertyChangeSupport(this);
+ private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
+ this);
boolean ignoreGapsInConsensusCalculation = false;
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;
/**
* Creates a new AlignViewport object.
- *
- * @param al DOCUMENT ME!
+ *
+ * @param al alignment to view
*/
public AlignViewport(AlignmentI al)
{
setAlignment(al);
init();
}
+ /**
+ * 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)
{
}
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)
+ {
+ hasHiddenColumns = true;
+ }
+ }
+ init();
+ }
void init()
{
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 + "");
String fontSize = Cache.getDefault("FONT_SIZE", "10");
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
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;
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;
}
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 (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)
/**
* DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
*/
public void setShowSequenceFeatures(boolean b)
{
return showSequenceFeatures;
}
- class ConservationThread
- extends Thread
+ class ConservationThread extends Thread
{
AlignmentPanel ap;
+
public ConservationThread(AlignmentPanel ap)
{
this.ap = ap;
{
if (ap != null)
{
- ap.repaint();
+ ap.paintAlignment(false);
}
Thread.sleep(200);
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
}
Conservation cons = new jalview.analysis.Conservation("All",
- jalview.schemes.ResidueProperties.propHash, 3,
- alignment.getSequences(), 0, alWidth - 1);
+ jalview.schemes.ResidueProperties.propHash, 3, alignment
+ .getSequences(), 0, alWidth - 1);
cons.calculate();
cons.verdict(false, ConsPercGaps);
minB = 0f;
maxR = 1.0f - minR;
maxG = 0.9f - minG;
- maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
+ maxB = 0f - minB; // scalable range for colouring both Conservation and
+ // Quality
float min = 0f;
float max = 11f;
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)));
+ 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();
+ 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)));
+ quality.annotations[i] = new Annotation(" ", String
+ .valueOf(value), ' ', value, new Color(minR
+ + (maxR * vprop), minG + (maxG * vprop), minB
+ + (maxB * vprop)));
}
}
- }
- catch (OutOfMemoryError error)
+ } 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);
- }
- });
+ new OOMWarning("calculating conservation", error);
conservation = null;
quality = null;
- System.out.println("Conservation calculation: " + error);
- System.gc();
-
}
UPDATING_CONSERVATION = false;
if (ap != null)
{
- ap.repaint();
+ ap.paintAlignment(true);
}
}
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)
{
}
/**
- * DOCUMENT ME!
+ * trigger update of consensus annotation
*/
public void updateConsensus(final AlignmentPanel ap)
{
consensusThread.start();
}
- class ConsensusThread
- extends Thread
+ class ConsensusThread extends Thread
{
AlignmentPanel ap;
+
public ConsensusThread(AlignmentPanel ap)
{
this.ap = ap;
{
if (ap != null)
{
- ap.repaint();
+ ap.paintAlignment(false);
}
Thread.sleep(200);
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
try
{
- int aWidth = alignment.getWidth();
+ int aWidth = (alignment != null) ? alignment.getWidth() : 0; // null
+ // pointer
+ // possibility
+ // here.
if (aWidth < 0)
{
return;
consensus.annotations = new Annotation[aWidth];
hconsensus = new Hashtable[aWidth];
- AAFrequency.calculate(alignment.getSequencesArray(),
- 0,
- alignment.getWidth(),
- hconsensus);
+ 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();
+ value = ((Float) hconsensus[i].get(AAFrequency.PID_NOGAPS))
+ .floatValue();
}
else
{
- value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)).
- floatValue();
+ value = ((Float) hconsensus[i].get(AAFrequency.PID_GAPS))
+ .floatValue();
}
- String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();
- String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";
+ String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE)
+ .toString();
+ String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE)
+ + " ";
if (maxRes.length() > 1)
{
maxRes = "+";
}
- mouseOver += ( (int) value + "%");
+ mouseOver += ((int) value + "%");
consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
- value);
+ value);
}
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;
if (ap != null)
{
- ap.repaint();
+ ap.paintAlignment(true);
}
}
}
/**
- * get the consensus sequence as displayed under the PID consensus annotation row.
+ * get the consensus sequence as displayed under the PID consensus annotation
+ * row.
+ *
* @return consensus sequence as a new sequence object
*/
public SequenceI getConsensusSeq()
}
SequenceI sq = new Sequence("Consensus", seqs.toString());
- sq.setDescription("Percentage Identity Consensus " +
- ( (ignoreGapsInConsensusCalculation) ? " without gaps" :
- ""));
+ sq.setDescription("Percentage Identity Consensus "
+ + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
return sq;
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public SequenceGroup getSelectionGroup()
/**
* DOCUMENT ME!
- *
- * @param sg DOCUMENT ME!
+ *
+ * @param sg
+ * DOCUMENT ME!
*/
public void setSelectionGroup(SequenceGroup sg)
{
- selectionGroup = sg;
+ selectionGroup = sg;
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean getConservationSelected()
/**
* DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
*/
public void setConservationSelected(boolean b)
{
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean getAbovePIDThreshold()
/**
* DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
*/
public void setAbovePIDThreshold(boolean b)
{
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getStartRes()
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getEndRes()
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getStartSeq()
/**
* DOCUMENT ME!
- *
- * @param cs DOCUMENT ME!
+ *
+ * @param cs
+ * DOCUMENT ME!
*/
public void setGlobalColourScheme(ColourSchemeI cs)
{
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public ColourSchemeI getGlobalColourScheme()
/**
* DOCUMENT ME!
- *
- * @param res DOCUMENT ME!
+ *
+ * @param res
+ * DOCUMENT ME!
*/
public void setStartRes(int res)
{
/**
* DOCUMENT ME!
- *
- * @param seq DOCUMENT ME!
+ *
+ * @param seq
+ * DOCUMENT ME!
*/
public void setStartSeq(int seq)
{
/**
* 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;
}
/**
* DOCUMENT ME!
- *
- * @param seq DOCUMENT ME!
+ *
+ * @param seq
+ * DOCUMENT ME!
*/
public void setEndSeq(int seq)
{
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getEndSeq()
/**
* DOCUMENT ME!
- *
- * @param f DOCUMENT ME!
+ *
+ * @param f
+ * DOCUMENT ME!
*/
public void setFont(Font f)
{
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public Font getFont()
/**
* DOCUMENT ME!
- *
- * @param w DOCUMENT ME!
+ *
+ * @param w
+ * DOCUMENT ME!
*/
public void setCharWidth(int w)
{
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getCharWidth()
/**
* DOCUMENT ME!
- *
- * @param h DOCUMENT ME!
+ *
+ * @param h
+ * DOCUMENT ME!
*/
public void setCharHeight(int h)
{
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getCharHeight()
/**
* DOCUMENT ME!
- *
- * @param w DOCUMENT ME!
+ *
+ * @param w
+ * DOCUMENT ME!
*/
public void setWrappedWidth(int w)
{
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getWrappedWidth()
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public AlignmentI getAlignment()
/**
* DOCUMENT ME!
- *
- * @param align DOCUMENT ME!
+ *
+ * @param align
+ * DOCUMENT ME!
*/
public void setAlignment(AlignmentI align)
{
+ if (alignment != null && alignment.getCodonFrames() != null)
+ {
+ StructureSelectionManager.getStructureSelectionManager()
+ .removeMappings(alignment.getCodonFrames());
+ }
this.alignment = align;
+ if (alignment.getCodonFrames() != null)
+ {
+ StructureSelectionManager.getStructureSelectionManager().addMappings(
+ alignment.getCodonFrames());
+ }
}
/**
* DOCUMENT ME!
- *
- * @param state DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
*/
public void setWrapAlignment(boolean state)
{
/**
* DOCUMENT ME!
- *
- * @param state DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
*/
public void setShowText(boolean state)
{
/**
* DOCUMENT ME!
- *
- * @param state DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
*/
public void setRenderGaps(boolean state)
{
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean getColourText()
/**
* DOCUMENT ME!
- *
- * @param state DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
*/
public void setColourText(boolean state)
{
/**
* DOCUMENT ME!
- *
- * @param state DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
*/
public void setShowBoxes(boolean state)
{
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean getWrapAlignment()
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean getShowText()
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean getShowBoxes()
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public char getGapCharacter()
/**
* DOCUMENT ME!
- *
- * @param gap DOCUMENT ME!
+ *
+ * @param gap
+ * DOCUMENT ME!
*/
public void setGapCharacter(char gap)
{
/**
* DOCUMENT ME!
- *
- * @param thresh DOCUMENT ME!
+ *
+ * @param thresh
+ * DOCUMENT ME!
*/
public void setThreshold(int thresh)
{
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getThreshold()
/**
* DOCUMENT ME!
- *
- * @param inc DOCUMENT ME!
+ *
+ * @param inc
+ * DOCUMENT ME!
*/
public void setIncrement(int inc)
{
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getIncrement()
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public ColumnSelection getColumnSelection()
/**
* DOCUMENT ME!
- *
- * @param tree DOCUMENT ME!
+ *
+ * @param tree
+ * DOCUMENT ME!
*/
public void setCurrentTree(NJTree tree)
{
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public NJTree getCurrentTree()
/**
* DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
*/
public void setColourAppliesToAllGroups(boolean b)
{
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean getColourAppliesToAllGroups()
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean getShowJVSuffix()
/**
* DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
*/
public void setShowJVSuffix(boolean b)
{
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean getShowAnnotation()
/**
* DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
*/
public void setShowAnnotation(boolean b)
{
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean getScaleAboveWrapped()
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean getScaleLeftWrapped()
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean getScaleRightWrapped()
/**
* DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
*/
public void setScaleAboveWrapped(boolean b)
{
/**
* DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
*/
public void setScaleLeftWrapped(boolean b)
{
/**
* DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
*/
public void setScaleRightWrapped(boolean b)
{
/**
* 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);
}
if (globalColourScheme != null)
{
globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
- ignoreGapsInConsensusCalculation);
+ ignoreGapsInConsensusCalculation);
}
}
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++)
seqs[index++] = sg.getSequenceAt(i);
}
}
-
+ sg.setSeqrep(repSequence);
+ sg.setHidereps(true);
hideSequence(seqs);
}
public void hideAllSelectedSeqs()
{
- if (selectionGroup == null)
+ if (selectionGroup == null || selectionGroup.getSize() < 1)
{
return;
}
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)
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)
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;
}
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()
{
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
{
}
/**
- * 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.
+ * 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;
+ if (selectionGroup == null)
+ {
+ sequences = alignment.getSequencesArray();
+ }
+ else
+ {
+ sequences = selectionGroup.getSequencesInOrder(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)
+ public jalview.datamodel.CigarArray getViewAsCigars(
+ boolean selectedRegionOnly)
{
CigarArray selection = null;
SequenceI[] seqs = null;
iSize = selectionGroup.getSize();
seqs = selectionGroup.getSequencesInOrder(alignment);
start = selectionGroup.getStartRes();
- end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
+ end = selectionGroup.getEndRes(); // inclusive for start and end in
+ // SeqCigar constructor
}
else
{
}
/**
- * 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
* @return AlignmentView
*/
jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly)
{
// JBPNote:
- // this is here because the AlignmentView constructor modifies the CigarArray
+ // 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);
+ (selectedOnly && selectionGroup != null) ? selectionGroup
+ .getStartRes() : 0);
}
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.
+ * 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)
return selection;
}
+ public int[][] getVisibleRegionBoundaries(int min, int max)
+ {
+ Vector regions = new Vector();
+ int start = min;
+ int end = max;
+
+ do
+ {
+ if (hasHiddenColumns)
+ {
+ if (start == 0)
+ {
+ start = colSel.adjustForHiddenColumns(start);
+ }
+
+ end = colSel.getHiddenBoundaryRight(start);
+ if (start == end)
+ {
+ end = max;
+ }
+ if (end > max)
+ {
+ end = max;
+ }
+ }
+
+ regions.addElement(new int[]
+ { start, end });
+
+ if (hasHiddenColumns)
+ {
+ start = colSel.adjustForHiddenColumns(end);
+ start = colSel.getHiddenBoundaryLeft(start) + 1;
+ }
+ } while (end < max);
+
+ int[][] startEnd = new int[regions.size()][2];
+
+ regions.copyInto(startEnd);
+
+ return startEnd;
+
+ }
+
public boolean getShowHiddenMarkers()
{
return showHiddenMarkers;
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)
updateConservation(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)
{
if (cs instanceof ClustalxColourScheme)
{
- ( (ClustalxColourScheme) cs).
- resetClustalX(alignment.getSequences(),
- alignment.getWidth());
+ ((ClustalxColourScheme) cs).resetClustalX(alignment.getSequences(),
+ alignment.getWidth());
}
cs.setConsensus(hconsensus);
{
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);
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();
}
}
}
+ /**
+ * 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;
+ /**
+ * checks current SelectionGroup against record of last hash value, and updates record.
+ * @return true if SelectionGroup changed since last call
+ */
+ boolean isSelectionGroupChanged() {
+ int hc=(selectionGroup==null) ? -1 : selectionGroup.hashCode();
+ if (hc!=sgrouphash)
+ {
+ sgrouphash = hc;
+ return true;
+ }
+ return false;
+ }
+ /**
+ * checks current colsel against record of last hash value, and updates record.
+ * @return true if colsel changed since last call
+ */
+ boolean isColSelChanged() {
+ int hc=(colSel==null) ? -1 : colSel.hashCode();
+ if (hc!=colselhash)
+ {
+ colselhash = hc;
+ return true;
+ }
+ return false;
+ }
+ public void sendSelection()
+ {
+ jalview.structure.StructureSelectionManager.getStructureSelectionManager().sendSelection(new SequenceGroup(getSelectionGroup()), new ColumnSelection(getColumnSelection()), this);
+ }
+
}