X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=c22a37dca5ee02a31678e681488f9508ac9fa23f;hb=90ae01c1c1504e0ae42817f78116f1d35b317c47;hp=a2d5ec27055d1ce3a5f6747c79e961f02fabebe8;hpb=a4833a9c3e15e416598b61e6887ee5743c3c2734;p=jalview.git
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
old mode 100755
new mode 100644
index a2d5ec2..c22a37d
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,1896 +1,1114 @@
- /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * 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
- * as published by the Free Software Foundation; either version 2
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
- *
- * 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-
-import jalview.bin.*;
-
-import jalview.datamodel.*;
-
-import jalview.schemes.*;
+import jalview.analysis.AlignmentUtils;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.analysis.TreeModel;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureColourI;
+import jalview.api.FeatureSettingsModelI;
+import jalview.api.FeaturesDisplayedI;
+import jalview.api.ViewStyleI;
+import jalview.bin.Cache;
+import jalview.commands.CommandI;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.ResidueShader;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.ResidueColourScheme;
+import jalview.schemes.UserColourScheme;
+import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.ws.params.AutoCalcSetting;
+
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Rectangle;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.JInternalFrame;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
- * @version $Revision$
+ * @version $Revision: 1.141 $
*/
-public class AlignViewport
+public class AlignViewport extends AlignmentViewport
+ 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;
-
- // The following vector holds the features which are
- // currently visible, in the correct order or rendering
- Hashtable featuresDisplayed = null;
-
-
- /** DOCUMENT ME!! */
- public Hashtable [] hconsensus;
- AlignmentAnnotation consensus;
- AlignmentAnnotation conservation;
- AlignmentAnnotation quality;
- boolean autoCalculateConsensus = true;
-
- /** DOCUMENT ME!! */
- public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
-
- // JBPNote Prolly only need this in the applet version.
- private java.beans.PropertyChangeSupport changeSupport = new java.beans.
- PropertyChangeSupport(this);
-
- boolean ignoreGapsInConsensusCalculation = false;
-
- boolean isDataset = false;
-
- boolean antiAlias = false;
-
- boolean padGaps = false;
-
- Rectangle explodedPosition;
-
- String viewName;
-
- String sequenceSetID;
-
- boolean gatherViewsHere = false;
-
- Stack historyList = new Stack();
- Stack redoList = new Stack();
-
- Hashtable sequenceColours;
-
- int thresholdTextColour = 0;
- Color textColour = Color.black;
- Color textColour2 = Color.white;
-
- boolean rightAlignIds = false;
-
- Hashtable hiddenRepSequences;
-
-
- /**
- * Creates a new AlignViewport object.
- *
- * @param al DOCUMENT ME!
- */
- 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();
- }
-
- void init()
- {
- this.startRes = 0;
- this.endRes = alignment.getWidth() - 1;
- this.startSeq = 0;
- this.endSeq = alignment.getHeight() - 1;
-
- antiAlias = Cache.getDefault("ANTI_ALIAS", false);
-
- showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
- showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
-
- rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
-
- autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
-
- padGaps = Cache.getDefault("PAD_GAPS", true);
-
- String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
- String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
- String fontSize = Cache.getDefault("FONT_SIZE", "10");
-
- seqNameItalics = Cache.getDefault("ID_ITALICS", true);
-
- int style = 0;
-
- if (fontStyle.equals("bold"))
- {
- 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) );
-
-
- // 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);
- }
-
- if (Cache.getDefault("SHOW_QUALITY", true))
- {
- quality = new AlignmentAnnotation("Quality",
- "Alignment Quality based on Blosum62 scores",
- new Annotation[1],
- 0f,
- 11f,
- AlignmentAnnotation.BAR_GRAPH);
- quality.hasText = true;
- quality.autoCalculated=true;
-
- alignment.addAnnotation(quality);
- }
- }
-
- consensus = new AlignmentAnnotation("Consensus", "PID",
- new Annotation[1], 0f, 100f,
- AlignmentAnnotation.BAR_GRAPH);
- consensus.hasText = true;
- consensus.autoCalculated=true;
-
- if (Cache.getDefault("SHOW_IDENTITY", true))
- {
- alignment.addAnnotation(consensus);
- }
- }
-
- if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
- {
- globalColourScheme = ColourSchemeProperty.getColour(alignment,
- jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
-
- if (globalColourScheme instanceof UserColourScheme)
- {
- globalColourScheme = UserDefinedColours.loadDefaultColours();
- ( (UserColourScheme) globalColourScheme).setThreshold(0,
- getIgnoreGapsConsensus());
- }
-
- if (globalColourScheme != null)
- {
- globalColourScheme.setConsensus(hconsensus);
- }
- }
-
- wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
- }
-
-
-
- /**
- * DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
- */
- public void setShowSequenceFeatures(boolean b)
- {
- showSequenceFeatures = b;
- }
-
- public boolean getShowSequenceFeatures()
- {
- return showSequenceFeatures;
- }
-
- class ConservationThread
- extends Thread
- {
- AlignmentPanel ap;
- public ConservationThread(AlignmentPanel ap)
- {
- this.ap = ap;
- }
-
- public void run()
- {
- try
- {
- updatingConservation = true;
-
- while (UPDATING_CONSERVATION)
- {
- try
- {
- if (ap != null)
- {
- ap.paintAlignment(false);
- }
- Thread.sleep(200);
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- UPDATING_CONSERVATION = true;
-
-
- int alWidth = alignment.getWidth();
- if(alWidth<0)
- {
- return;
- }
-
- Conservation cons = new jalview.analysis.Conservation("All",
- jalview.schemes.ResidueProperties.propHash, 3,
- alignment.getSequences(), 0, alWidth -1);
-
- cons.calculate();
- cons.verdict(false, ConsPercGaps);
-
- if (quality!=null)
- {
- cons.findQuality();
- }
-
- char [] sequence = cons.getConsSequence().getSequence();
- float minR;
- float minG;
- float minB;
- float maxR;
- float maxG;
- float maxB;
- minR = 0.3f;
- minG = 0.0f;
- minB = 0f;
- maxR = 1.0f - minR;
- maxG = 0.9f - minG;
- maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
-
- float min = 0f;
- float max = 11f;
- float qmin = 0f;
- float qmax = 0f;
-
- char c;
-
- conservation.annotations = new Annotation[alWidth];
-
- if (quality!=null)
- {
- quality.graphMax = cons.qualityRange[1].floatValue();
- quality.annotations = new Annotation[alWidth];
- qmin = cons.qualityRange[0].floatValue();
- qmax = cons.qualityRange[1].floatValue();
- }
-
- for (int i = 0; i < alWidth; i++)
- {
- float value = 0;
-
- c = sequence[i];
-
- if (Character.isDigit(c))
- {
- value = (int) (c - '0');
- }
- else if (c == '*')
- {
- value = 11;
- }
- else if (c == '+')
- {
- value = 10;
- }
-
- float vprop = value - min;
- vprop /= max;
- conservation.annotations[i] =
- new Annotation(String.valueOf(c),
- String.valueOf(value), ' ', value,
- new Color(minR + (maxR * vprop),
- minG + (maxG * vprop),
- minB + (maxB * vprop)));
-
- // Quality calc
- if (quality!=null)
- {
- value = ( (Double) cons.quality.get(i)).floatValue();
- vprop = value - qmin;
- vprop /= qmax;
- quality.annotations[i] = new Annotation(" ", String.valueOf(value),
- ' ',
- value,
- new Color(minR + (maxR * vprop),
- minG + (maxG * vprop),
- minB + (maxB * vprop)));
- }
- }
- }
- catch (OutOfMemoryError error)
- {
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
+ Font font;
+ TreeModel currentTree = null;
- public void run()
- {
- javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Out of memory calculating conservation!!"
- +
- "\nSee help files for increasing Java Virtual Machine memory."
- , "Out of memory",
- javax.swing.JOptionPane.WARNING_MESSAGE);
- }
- });
-
- conservation = null;
- quality = null;
-
- System.out.println("Conservation calculation: " + error);
- System.gc();
-
- }
-
- UPDATING_CONSERVATION = false;
- updatingConservation = false;
-
- if(ap!=null)
- {
- ap.paintAlignment(true);
- }
-
- }
- }
-
-
- ConservationThread conservationThread;
-
- ConsensusThread consensusThread;
-
- boolean consUpdateNeeded = false;
-
- static boolean UPDATING_CONSENSUS = false;
-
- static boolean UPDATING_CONSERVATION = false;
-
- boolean updatingConsensus = false;
-
- boolean updatingConservation = false;
-
- /**
- * DOCUMENT ME!
- */
- public void updateConservation(final AlignmentPanel ap)
- {
- if (alignment.isNucleotide() || conservation==null)
- {
- return;
- }
-
- conservationThread = new ConservationThread(ap);
- conservationThread.start();
- }
-
- /**
- * DOCUMENT ME!
- */
- public void updateConsensus(final AlignmentPanel ap)
- {
- consensusThread = new ConsensusThread(ap);
- consensusThread.start();
- }
-
- class ConsensusThread
- extends Thread
- {
- AlignmentPanel ap;
- public ConsensusThread(AlignmentPanel ap)
- {
- this.ap = ap;
- }
- public void run()
- {
- updatingConsensus = true;
- while (UPDATING_CONSENSUS)
- {
- try
- {
- if (ap != null)
- {
- ap.paintAlignment(false);
- }
-
- Thread.sleep(200);
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
-
- UPDATING_CONSENSUS = true;
-
- try
- {
- int aWidth = (alignment!=null) ? alignment.getWidth() : 0; // null pointer possibility here.
- if(aWidth<0)
- {
- return;
- }
-
- consensus.annotations = null;
- consensus.annotations = new Annotation[aWidth];
-
-
- hconsensus = new Hashtable[aWidth];
- AAFrequency.calculate(alignment.getSequencesArray(),
- 0,
- alignment.getWidth(),
- hconsensus);
+ boolean cursorMode = false;
- 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) + " ";
+ boolean antiAlias = false;
- if (maxRes.length() > 1)
- {
- mouseOver = "[" + maxRes + "] ";
- maxRes = "+";
- }
-
- mouseOver += ( (int) value + "%");
- consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
- value);
- }
-
-
- if (globalColourScheme != null)
- {
- globalColourScheme.setConsensus(hconsensus);
- }
+ private Rectangle explodedGeometry;
- }
- catch (OutOfMemoryError error)
- {
- alignment.deleteAnnotation(consensus);
+ String viewName;
- 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);
- }
- });
+ /*
+ * Flag set true on the view that should 'gather' multiple views of the same
+ * sequence set id when a project is reloaded. Set false on all views when
+ * they are 'exploded' into separate windows. Set true on the current view
+ * when 'Gather' is performed, and also on the first tab when the first new
+ * view is created.
+ */
+ private boolean gatherViewsHere = false;
- System.out.println("Consensus calculation: " + error);
- System.gc();
- }
- UPDATING_CONSENSUS = false;
- updatingConsensus = false;
+ private AnnotationColumnChooser annotationColumnSelectionState;
- if (ap != null)
- {
- ap.paintAlignment(true);
- }
- }
- }
- /**
- * get the consensus sequence as displayed under the PID consensus annotation row.
- * @return consensus sequence as a new sequence object
- */
- public SequenceI getConsensusSeq()
+ /**
+ * Creates a new AlignViewport object.
+ *
+ * @param al
+ * alignment to view
+ */
+ public AlignViewport(AlignmentI al)
{
- if (consensus==null)
- {
- updateConsensus(null);
- }
- if (consensus==null)
- {
- return null;
- }
- StringBuffer seqs=new StringBuffer();
- for (int i = 0; i < consensus.annotations.length; i++)
- {
- if (consensus.annotations[i] != null)
- {
- if (consensus.annotations[i].description.charAt(0) == '[')
- {
- seqs.append(consensus.annotations[i].description.charAt(1));
- }
- else
- {
- seqs.append(consensus.annotations[i].displayCharacter);
- }
- }
- }
-
- SequenceI sq = new Sequence("Consensus", seqs.toString());
- sq.setDescription("Percentage Identity Consensus " +
- ( (ignoreGapsInConsensusCalculation) ? " without gaps" :
- ""));
- return sq;
- }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public SequenceGroup getSelectionGroup()
- {
- return selectionGroup;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param sg DOCUMENT ME!
- */
- public void setSelectionGroup(SequenceGroup sg)
- {
- selectionGroup = sg;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getConservationSelected()
- {
- return conservationColourSelected;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
- */
- public void setConservationSelected(boolean b)
- {
- conservationColourSelected = b;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getAbovePIDThreshold()
- {
- return abovePIDThreshold;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
- */
- 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;
- }
+ super(al);
+ init();
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getStartSeq()
- {
- return startSeq;
- }
+ /**
+ * 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!
- *
- * @param cs DOCUMENT ME!
- */
- public void setGlobalColourScheme(ColourSchemeI cs)
+ public AlignViewport(AlignmentI al, String seqsetid, String viewid)
+ {
+ super(al);
+ sequenceSetID = seqsetid;
+ viewId = viewid;
+ // TODO remove these once 2.4.VAMSAS release finished
+ if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
{
- globalColourScheme = cs;
+ Cache.log.debug(
+ "Setting viewport's sequence set id : " + sequenceSetID);
}
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public ColourSchemeI getGlobalColourScheme()
+ if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
{
- return globalColourScheme;
+ Cache.log.debug("Setting viewport's view id : " + viewId);
}
+ init();
- /**
- * 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)
+ /**
+ * Create a new AlignViewport with hidden regions
+ *
+ * @param al
+ * AlignmentI
+ * @param hiddenColumns
+ * ColumnSelection
+ */
+ public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns)
+ {
+ super(al);
+ if (hiddenColumns != null)
{
- this.startSeq = seq;
+ al.setHiddenColumns(hiddenColumns);
}
+ init();
+ }
- /**
- * 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;
- }
+ /**
+ * New viewport with hidden columns and an existing sequence set id
+ *
+ * @param al
+ * @param hiddenColumns
+ * @param seqsetid
+ * (may be null)
+ */
+ public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,
+ String seqsetid)
+ {
+ this(al, hiddenColumns, seqsetid, null);
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getEndSeq()
+ /**
+ * 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, HiddenColumns hiddenColumns,
+ String seqsetid, String viewid)
+ {
+ super(al);
+ sequenceSetID = seqsetid;
+ viewId = viewid;
+ // TODO remove these once 2.4.VAMSAS release finished
+ if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
{
- return endSeq;
+ Cache.log.debug(
+ "Setting viewport's sequence set id : " + sequenceSetID);
}
-
- /**
- * DOCUMENT ME!
- *
- * @param f DOCUMENT ME!
- */
- public void setFont(Font f)
+ if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
{
- font = f;
-
- Container c = new Container();
-
- java.awt.FontMetrics fm = c.getFontMetrics(font);
- setCharHeight(fm.getHeight());
- setCharWidth(fm.charWidth('M'));
- validCharWidth = true;
+ Cache.log.debug("Setting viewport's view id : " + viewId);
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Font getFont()
+ if (hiddenColumns != null)
{
- return font;
+ al.setHiddenColumns(hiddenColumns);
}
+ init();
+ }
- /**
- * DOCUMENT ME!
- *
- * @param w DOCUMENT ME!
- */
- public void setCharWidth(int w)
- {
- this.charWidth = w;
- }
+ /**
+ * Apply any settings saved in user preferences
+ */
+ private void applyViewProperties()
+ {
+ antiAlias = Cache.getDefault("ANTI_ALIAS", false);
+
+ viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true));
+ setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
+
+ setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
+ setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false));
+ autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
+
+ setPadGaps(Cache.getDefault("PAD_GAPS", true));
+ setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
+ setShowDBRefs(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
+ viewStyle.setSeqNameItalics(Cache.getDefault("ID_ITALICS", true));
+ viewStyle.setWrapAlignment(Cache.getDefault("WRAP_ALIGNMENT", false));
+ viewStyle.setShowUnconserved(
+ Cache.getDefault("SHOW_UNCONSERVED", false));
+ sortByTree = Cache.getDefault("SORT_BY_TREE", false);
+ followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true);
+ sortAnnotationsBy = SequenceAnnotationOrder
+ .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
+ SequenceAnnotationOrder.NONE.name()));
+ showAutocalculatedAbove = Cache
+ .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
+ viewStyle.setScaleProteinAsCdna(
+ Cache.getDefault(Preferences.SCALE_PROTEIN_TO_CDNA, true));
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getCharWidth()
- {
- return charWidth;
- }
+ void init()
+ {
+ applyViewProperties();
- /**
- * DOCUMENT ME!
- *
- * @param h DOCUMENT ME!
- */
- public void setCharHeight(int h)
- {
- this.charHeight = h;
- }
+ String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
+ String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
+ String fontSize = Cache.getDefault("FONT_SIZE", "10");
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getCharHeight()
- {
- return charHeight;
- }
+ int style = 0;
- /**
- * DOCUMENT ME!
- *
- * @param w DOCUMENT ME!
- */
- public void setWrappedWidth(int w)
+ if (fontStyle.equals("bold"))
{
- this.wrappedWidth = w;
+ style = 1;
}
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getWrappedWidth()
+ else if (fontStyle.equals("italic"))
{
- return wrappedWidth;
+ style = 2;
}
+ setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public AlignmentI getAlignment()
- {
- return alignment;
- }
+ alignment
+ .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
- /**
- * DOCUMENT ME!
- *
- * @param align DOCUMENT ME!
- */
- public void setAlignment(AlignmentI align)
+ // We must set conservation and consensus before setting colour,
+ // as Blosum and Clustal require this to be done
+ if (hconsensus == null && !isDataset)
{
- if (alignment!=null && alignment.getCodonFrames()!=null)
+ if (!alignment.isNucleotide())
{
- StructureSelectionManager.getStructureSelectionManager().removeMappings(alignment.getCodonFrames());
+ showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
+ showQuality = Cache.getDefault("SHOW_QUALITY", true);
+ showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
+ false);
}
- this.alignment = align;
- if (alignment.getCodonFrames()!=null)
- {
- StructureSelectionManager.getStructureSelectionManager().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;
- }
+ showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
+ true);
+ showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
+ normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
+ false);
+ showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
+ showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
- /**
- * DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
- */
- public void setColourAppliesToAllGroups(boolean b)
- {
- colourAppliesToAllGroups = b;
+ showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
}
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getColourAppliesToAllGroups()
+ initAutoAnnotation();
+ String colourProperty = alignment.isNucleotide()
+ ? Preferences.DEFAULT_COLOUR_NUC
+ : Preferences.DEFAULT_COLOUR_PROT;
+ String schemeName = Cache.getProperty(colourProperty);
+ if (schemeName == null)
{
- return colourAppliesToAllGroups;
+ // only DEFAULT_COLOUR available in Jalview before 2.9
+ schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR,
+ ResidueColourScheme.NONE);
}
+ ColourSchemeI colourScheme = ColourSchemeProperty
+ .getColourScheme(alignment, schemeName);
+ residueShading = new ResidueShader(colourScheme);
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getShowJVSuffix()
+ if (colourScheme instanceof UserColourScheme)
{
- return showJVSuffix;
+ residueShading = new ResidueShader(
+ UserDefinedColours.loadDefaultColours());
+ residueShading.setThreshold(0, isIgnoreGapsConsensus());
}
- /**
- * DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
- */
- public void setShowJVSuffix(boolean b)
+ if (residueShading != null)
{
- showJVSuffix = b;
+ residueShading.setConsensus(hconsensus);
}
+ }
+ boolean validCharWidth;
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getShowAnnotation()
- {
- return showAnnotation;
- }
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public void setFont(Font f, boolean setGrid)
+ {
+ font = f;
- /**
- * DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
- */
- public void setShowAnnotation(boolean b)
- {
- showAnnotation = b;
- }
+ Container c = new Container();
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getScaleAboveWrapped()
+ if (setGrid)
{
- return scaleAboveWrapped;
+ FontMetrics fm = c.getFontMetrics(font);
+ int ww = fm.charWidth('M');
+ setCharHeight(fm.getHeight());
+ setCharWidth(ww);
}
+ viewStyle.setFontName(font.getName());
+ viewStyle.setFontStyle(font.getStyle());
+ viewStyle.setFontSize(font.getSize());
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getScaleLeftWrapped()
- {
- return scaleLeftWrapped;
- }
+ validCharWidth = true;
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getScaleRightWrapped()
- {
- return scaleRightWrapped;
- }
+ @Override
+ public void setViewStyle(ViewStyleI settingsForView)
+ {
+ super.setViewStyle(settingsForView);
+ setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
+ viewStyle.getFontSize()), false);
+ }
- /**
- * DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
- */
- public void setScaleAboveWrapped(boolean b)
- {
- scaleAboveWrapped = b;
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Font getFont()
+ {
+ return font;
+ }
- /**
- * DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
- */
- public void setScaleLeftWrapped(boolean b)
- {
- scaleLeftWrapped = b;
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param align
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setAlignment(AlignmentI align)
+ {
+ replaceMappings(align);
+ super.setAlignment(align);
+ }
- /**
- * DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
- */
- public void setScaleRightWrapped(boolean b)
- {
- scaleRightWrapped = b;
- }
+ /**
+ * Replace any codon mappings for this viewport with those for the given
+ * viewport
+ *
+ * @param align
+ */
+ public void replaceMappings(AlignmentI align)
+ {
- /**
- * Property change listener for changes in alignment
- *
- * @param listener DOCUMENT ME!
+ /*
+ * Deregister current mappings (if any)
*/
- public void addPropertyChangeListener(
- java.beans.PropertyChangeListener listener)
- {
- changeSupport.addPropertyChangeListener(listener);
- }
+ deregisterMappings();
- /**
- * DOCUMENT ME!
- *
- * @param listener DOCUMENT ME!
+ /*
+ * Register new mappings (if any)
*/
- public void removePropertyChangeListener(
- java.beans.PropertyChangeListener listener)
+ if (align != null)
{
- changeSupport.removePropertyChangeListener(listener);
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ ssm.registerMappings(align.getCodonFrames());
}
- /**
- * Property change listener for changes in alignment
- *
- * @param prop DOCUMENT ME!
- * @param oldvalue DOCUMENT ME!
- * @param newvalue DOCUMENT ME!
+ /*
+ * replace mappings on our alignment
*/
- public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
+ if (alignment != null && align != null)
{
- changeSupport.firePropertyChange(prop, oldvalue, newvalue);
+ alignment.setCodonFrames(align.getCodonFrames());
}
+ }
- public void setIgnoreGapsConsensus(boolean b, AlignmentPanel ap)
+ protected void deregisterMappings()
+ {
+ AlignmentI al = getAlignment();
+ if (al != null)
{
- ignoreGapsInConsensusCalculation = b;
- updateConsensus(ap);
- if(globalColourScheme!=null)
+ List mappings = al.getCodonFrames();
+ if (mappings != null)
{
- globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
- ignoreGapsInConsensusCalculation);
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ for (AlignedCodonFrame acf : mappings)
+ {
+ if (noReferencesTo(acf))
+ {
+ ssm.deregisterMapping(acf);
+ }
+ }
}
}
+ }
- public boolean getIgnoreGapsConsensus()
- {
- return ignoreGapsInConsensusCalculation;
- }
-
- public void setDataset(boolean b)
- {
- isDataset = b;
- }
-
- public boolean isDataset()
- {
- return isDataset;
- }
-
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public char getGapCharacter()
+ {
+ return getAlignment().getGapCharacter();
+ }
- public void hideSelectedColumns()
- {
- if (colSel.size() < 1)
+ /**
+ * DOCUMENT ME!
+ *
+ * @param gap
+ * DOCUMENT ME!
+ */
+ public void setGapCharacter(char gap)
+ {
+ if (getAlignment() != null)
{
- return;
+ getAlignment().setGapCharacter(gap);
}
+ }
- colSel.hideSelectedColumns();
- setSelectionGroup(null);
-
- hasHiddenColumns = true;
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param tree
+ * DOCUMENT ME!
+ */
+ public void setCurrentTree(TreeModel tree)
+ {
+ currentTree = tree;
+ }
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public TreeModel getCurrentTree()
+ {
+ return currentTree;
+ }
- public void hideColumns(int start, int end)
- {
- if(start==end)
+ /**
+ * returns the visible column regions of the alignment
+ *
+ * @param selectedRegionOnly
+ * true to just return the contigs intersecting with the selected
+ * area
+ * @return
+ */
+ public int[] getViewAsVisibleContigs(boolean selectedRegionOnly)
+ {
+ int[] viscontigs = null;
+ int start = 0, end = 0;
+ if (selectedRegionOnly && selectionGroup != null)
{
- colSel.hideColumns(start);
+ start = selectionGroup.getStartRes();
+ end = selectionGroup.getEndRes() + 1;
}
- else
+ else
{
- colSel.hideColumns(start, end);
- }
-
- hasHiddenColumns = true;
+ end = alignment.getWidth();
}
+ viscontigs = alignment.getHiddenColumns().getVisibleContigs(start, end);
+ return viscontigs;
+ }
- public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
- {
- int sSize = sg.getSize();
- if(sSize < 2)
+ /**
+ * get hash of undo and redo list for the alignment
+ *
+ * @return long[] { historyList.hashCode, redoList.hashCode };
+ */
+ public long[] getUndoRedoHash()
+ {
+ // TODO: JAL-1126
+ if (historyList == null || redoList == null)
{
- return;
+ return new long[] { -1, -1 };
}
+ return new long[] { historyList.hashCode(), this.redoList.hashCode() };
+ }
- if(hiddenRepSequences==null)
+ /**
+ * test if a particular set of hashcodes are different to the hashcodes for
+ * the undo and redo list.
+ *
+ * @param undoredo
+ * the stored set of hashcodes as returned by getUndoRedoHash
+ * @return true if the hashcodes differ (ie the alignment has been edited) or
+ * the stored hashcode array differs in size
+ */
+ public boolean isUndoRedoHashModified(long[] undoredo)
+ {
+ if (undoredo == null)
{
- hiddenRepSequences = new Hashtable();
+ return true;
}
-
- hiddenRepSequences.put(repSequence, sg);
-
- //Hide all sequences except the repSequence
- SequenceI [] seqs = new SequenceI[sSize-1];
- int index = 0;
- for(int i=0; i0)
- {
- if(selectionGroup==null)
- {
- selectionGroup = new SequenceGroup();
- selectionGroup.setEndRes(alignment.getWidth()-1);
- }
-
- for (int t = 0; t < tmp.size(); t++)
- {
- selectionGroup.addSequence(
- (SequenceI) tmp.elementAt(t), false
- );
- }
- firePropertyChange("alignment", null, alignment.getSequences());
- }
-
- if(alignment.getHiddenSequences().getSize()<1)
- {
- hasHiddenRows = false;
- }
+ public boolean getSortByTree()
+ {
+ return sortByTree;
}
- public void showColumn(int col)
- {
- colSel.revealHiddenColumns(col);
- if(colSel.getHiddenColumns()==null)
- {
- hasHiddenColumns = false;
- }
+ public void setSortByTree(boolean sort)
+ {
+ sortByTree = sort;
}
- public void showAllHiddenColumns()
- {
- colSel.revealAllHiddenColumns();
- hasHiddenColumns = false;
- }
+ /**
+ * Returns the (Desktop) instance of the StructureSelectionManager
+ */
+ @Override
+ public StructureSelectionManager getStructureSelectionManager()
+ {
+ return StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ }
- public void showAllHiddenSeqs()
+ /**
+ *
+ * @param pdbEntries
+ * @return an array of SequenceI arrays, one for each PDBEntry, listing which
+ * sequences in the alignment hold a reference to it
+ */
+ public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
+ {
+ List seqvectors = new ArrayList();
+ for (PDBEntry pdb : pdbEntries)
{
- if(alignment.getHiddenSequences().getSize()>0)
+ List choosenSeqs = new ArrayList();
+ for (SequenceI sq : alignment.getSequences())
{
- if(selectionGroup==null)
+ Vector pdbRefEntries = sq.getDatasetSequence()
+ .getAllPDBEntries();
+ if (pdbRefEntries == null)
{
- selectionGroup = new SequenceGroup();
- selectionGroup.setEndRes(alignment.getWidth()-1);
+ continue;
}
- Vector tmp = alignment.getHiddenSequences().showAll(hiddenRepSequences);
- for(int t=0; t calcIdParams = new Hashtable();
+
+ public AutoCalcSetting getCalcIdSettingsFor(String calcId)
+ {
+ return calcIdParams.get(calcId);
+ }
+
+ public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings,
+ boolean needsUpdate)
+ {
+ calcIdParams.put(calcId, settings);
+ // TODO: create a restart list to trigger any calculations that need to be
+ // restarted after load
+ // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
+ if (needsUpdate)
{
- return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
+ Cache.log.debug("trigger update for " + calcId);
}
+ }
- /**
- * 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
+ /**
+ * Method called when another alignment's edit (or possibly other) command is
+ * broadcast to here.
+ *
+ * To allow for sequence mappings (e.g. protein to cDNA), we have to first
+ * 'unwind' the command on the source sequences (in simulation, not in fact),
+ * and then for each edit in turn:
+ *
+ * - compute the equivalent edit on the mapped sequences
+ * - apply the mapped edit
+ * - 'apply' the source edit to the working copy of the source
+ * sequences
+ *
+ *
+ * @param command
+ * @param undo
+ * @param ssm
+ */
+ @Override
+ public void mirrorCommand(CommandI command, boolean undo,
+ StructureSelectionManager ssm, VamsasSource source)
+ {
+ /*
+ * Do nothing unless we are a 'complement' of the source. May replace this
+ * with direct calls not via SSM.
*/
- public SequenceI[] getSelectionAsNewSequence()
- {
- SequenceI[] sequences;
-
- if (selectionGroup == null)
+ if (source instanceof AlignViewportI
+ && ((AlignViewportI) source).getCodingComplement() == this)
{
- sequences = alignment.getSequencesArray();
- AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
- for (int i=0; i last)
- {
- hideStart = last;
- }
- else
- {
- continue;
- }
- }
+ }
- if (hideStart>end)
- {
- break;
- }
+ /**
+ * Add the sequences from the given alignment to this viewport. Optionally,
+ * may give the user the option to open a new frame, or split panel, with cDNA
+ * and protein linked.
+ *
+ * @param toAdd
+ * @param title
+ */
+ public void addAlignment(AlignmentI toAdd, String title)
+ {
+ // TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different
- if (hideEnd>end)
- {
- hideEnd=end;
- }
+ // JBPComment: title is a largely redundant parameter at the moment
+ // JBPComment: this really should be an 'insert/pre/append' controller
+ // JBPComment: but the DNA/Protein check makes it a bit more complex
- if (hideStart>hideEnd)
- {
- break;
- }
- /**
- * form operations...
- */
- if (last max)
- {
- end = max;
- }
+ al.addSequence(seq);
}
+ }
- regions.addElement(new int[]
- {start, end});
+ ranges.setEndSeq(getAlignment().getHeight());
+ firePropertyChange("alignment", null, getAlignment().getSequences());
+ }
- if (hasHiddenColumns)
- {
- start = colSel.adjustForHiddenColumns(end);
- start = colSel.getHiddenBoundaryLeft(start) + 1;
- }
+ /**
+ * Show a dialog with the option to open and link (cDNA <-> protein) as a new
+ * alignment, either as a standalone alignment or in a split frame. Returns
+ * true if the new alignment was opened, false if not, because the user
+ * declined the offer.
+ *
+ * @param al
+ * @param title
+ */
+ protected boolean openLinkedAlignment(AlignmentI al, String title)
+ {
+ String[] options = new String[] { MessageManager.getString("action.no"),
+ MessageManager.getString("label.split_window"),
+ MessageManager.getString("label.new_window"), };
+ final String question = JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.open_split_window?"));
+ int response = JvOptionPane.showOptionDialog(Desktop.desktop, question,
+ MessageManager.getString("label.open_split_window"),
+ JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
+ options, options[0]);
+
+ if (response != 1 && response != 2)
+ {
+ return false;
}
- while (end < max);
+ final boolean openSplitPane = (response == 1);
+ final boolean openInNewWindow = (response == 2);
- int[][] startEnd = new int[regions.size()][2];
+ /*
+ * Identify protein and dna alignments. Make a copy of this one if opening
+ * in a new split pane.
+ */
+ AlignmentI thisAlignment = openSplitPane ? new Alignment(getAlignment())
+ : getAlignment();
+ AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
+ final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
- regions.copyInto(startEnd);
+ /*
+ * Map sequences. At least one should get mapped as we have already passed
+ * the test for 'mappability'. Any mappings made will be added to the
+ * protein alignment. Note creating dataset sequences on the new alignment
+ * is a pre-requisite for building mappings.
+ */
+ al.setDataset(null);
+ AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna);
- return startEnd;
+ /*
+ * Create the AlignFrame for the added alignment. If it is protein, mappings
+ * are registered with StructureSelectionManager as a side-effect.
+ */
+ AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ newAlignFrame.setTitle(title);
+ newAlignFrame.statusBar.setText(MessageManager
+ .formatMessage("label.successfully_loaded_file", new Object[]
+ { title }));
- }
+ // TODO if we want this (e.g. to enable reload of the alignment from file),
+ // we will need to add parameters to the stack.
+ // if (!protocol.equals(DataSourceType.PASTE))
+ // {
+ // alignFrame.setFileName(file, format);
+ // }
- public boolean getShowHiddenMarkers()
+ if (openInNewWindow)
{
- return showHiddenMarkers;
+ Desktop.addInternalFrame(newAlignFrame, title,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
}
- public void setShowHiddenMarkers(boolean show)
+ try
+ {
+ newAlignFrame.setMaximum(
+ jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+ } catch (java.beans.PropertyVetoException ex)
{
- showHiddenMarkers = show;
}
- public String getSequenceSetId()
+ if (openSplitPane)
{
- if(sequenceSetID==null)
- {
- sequenceSetID = alignment.hashCode()+"";
+ al.alignAs(thisAlignment);
+ protein = openSplitFrame(newAlignFrame, thisAlignment);
}
- return sequenceSetID;
- }
+ return true;
+ }
- public void alignmentChanged(AlignmentPanel ap)
- {
- if (padGaps)
- {
- alignment.padGaps();
- }
+ /**
+ * Helper method to open a new SplitFrame holding linked dna and protein
+ * alignments.
+ *
+ * @param newAlignFrame
+ * containing a new alignment to be shown
+ * @param complement
+ * cdna/protein complement alignment to show in the other split half
+ * @return the protein alignment in the split frame
+ */
+ protected AlignmentI openSplitFrame(AlignFrame newAlignFrame,
+ AlignmentI complement)
+ {
+ /*
+ * Make a new frame with a copy of the alignment we are adding to. If this
+ * is protein, the mappings to cDNA will be registered with
+ * StructureSelectionManager as a side-effect.
+ */
+ AlignFrame copyMe = new AlignFrame(complement, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ copyMe.setTitle(getAlignPanel().alignFrame.getTitle());
+
+ AlignmentI al = newAlignFrame.viewport.getAlignment();
+ final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
+ : newAlignFrame;
+ final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame : copyMe;
+ cdnaFrame.setVisible(true);
+ proteinFrame.setVisible(true);
+ String linkedTitle = MessageManager
+ .getString("label.linked_view_title");
+
+ /*
+ * Open in split pane. DNA sequence above, protein below.
+ */
+ JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
+ Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
+
+ return proteinFrame.viewport.getAlignment();
+ }
- if (hconsensus != null && autoCalculateConsensus)
- {
- updateConsensus(ap);
- updateConservation(ap);
- }
+ public AnnotationColumnChooser getAnnotationColumnSelectionState()
+ {
+ return annotationColumnSelectionState;
+ }
- //Reset endRes of groups if beyond alignment width
- int alWidth = alignment.getWidth();
- Vector groups = alignment.getGroups();
- if(groups!=null)
- {
- for(int i=0; ialWidth)
- {
- sg.setEndRes(alWidth-1);
- }
- }
- }
+ public void setAnnotationColumnSelectionState(
+ AnnotationColumnChooser currentAnnotationColumnSelectionState)
+ {
+ this.annotationColumnSelectionState = currentAnnotationColumnSelectionState;
+ }
- if(selectionGroup!=null && selectionGroup.getEndRes()>alWidth)
+ @Override
+ public void setIdWidth(int i)
+ {
+ super.setIdWidth(i);
+ AlignmentPanel ap = getAlignPanel();
+ if (ap != null)
{
- selectionGroup.setEndRes(alWidth-1);
+ // modify GUI elements to reflect geometry change
+ Dimension idw = getAlignPanel().getIdPanel().getIdCanvas()
+ .getPreferredSize();
+ idw.width = i;
+ getAlignPanel().getIdPanel().getIdCanvas().setPreferredSize(idw);
}
+ }
- resetAllColourSchemes();
-
- // alignment.adjustSequenceAnnotations();
- }
+ public Rectangle getExplodedGeometry()
+ {
+ return explodedGeometry;
+ }
+ public void setExplodedGeometry(Rectangle explodedPosition)
+ {
+ this.explodedGeometry = explodedPosition;
+ }
- void resetAllColourSchemes()
- {
- ColourSchemeI cs = globalColourScheme;
- if(cs!=null)
- {
- if (cs instanceof ClustalxColourScheme)
- {
- ( (ClustalxColourScheme) cs).
- resetClustalX(alignment.getSequences(),
- alignment.getWidth());
- }
+ public boolean isGatherViewsHere()
+ {
+ return gatherViewsHere;
+ }
- 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);
- }
- }
+ public void setGatherViewsHere(boolean gatherViewsHere)
+ {
+ this.gatherViewsHere = gatherViewsHere;
+ }
- int s, sSize = alignment.getGroups().size();
- for(s=0; s renderOrder = fr.getRenderOrder();
+ FeaturesDisplayedI displayed = fr.getFeaturesDisplayed();
+ displayed.clear();
+ // TODO this clears displayed.featuresRegistered - do we care?
+
+ /*
+ * set feature colour if specified by feature settings
+ * set visibility of all features
*/
- public int[] getViewAsVisibleContigs(boolean selectedRegionOnly) {
- int[] viscontigs=null;
- int start = 0, end = 0;
- if(selectedRegionOnly && selectionGroup!=null)
+ for (String type : renderOrder)
+ {
+ FeatureColourI preferredColour = featureSettings
+ .getFeatureColour(type);
+ if (preferredColour != null)
{
- start = selectionGroup.getStartRes();
- end = selectionGroup.getEndRes()+1;
+ fr.setColour(type, preferredColour);
}
- else
+ if (featureSettings.isFeatureDisplayed(type))
{
- end = alignment.getWidth();
+ displayed.setVisible(type);
}
- viscontigs = colSel.getVisibleContigs(start, end);
- return viscontigs;
}
- /**
- * get hash of undo and redo list for the alignment
- * @return long[] { historyList.hashCode, redoList.hashCode };
+
+ /*
+ * set visibility of feature groups
*/
- public long[] getUndoRedoHash()
+ for (String group : fr.getFeatureGroups())
{
- if (historyList==null || redoList==null)
- return new long[] { -1, -1};
- return new long[] { historyList.hashCode(), this.redoList.hashCode() };
+ fr.setGroupVisibility(group, featureSettings.isGroupDisplayed(group));
}
- /**
- * 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
+
+ /*
+ * order the features
*/
- public boolean isUndoRedoHashModified(long[] undoredo)
+ if (featureSettings.optimiseOrder())
{
- if (undoredo==null)
- {
- return true;
- }
- long[] cstate = getUndoRedoHash();
- if (cstate.length!=undoredo.length)
- { return true; }
-
- for (int i=0; i