X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=de8f310cf7b8b3f90de225275a725bd21741f184;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=d07b010ed81f4d75279ad3cd269f7fee8c107b77;hpb=5feda00b43b9156b7a86b232b63a5da0736113ee;p=jalview.git
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
old mode 100755
new mode 100644
index d07b010..de8f310
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,20 +1,20 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
*
- * 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 file is part of Jalview.
*
- * 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 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
/*
* Jalview - A Sequence Alignment Editor and Viewer
@@ -36,30 +36,43 @@
*/
package jalview.gui;
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-
-import jalview.bin.*;
-
-import jalview.datamodel.*;
-
-import jalview.schemes.*;
+import jalview.analysis.NJTree;
+import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.UserColourScheme;
import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.ws.params.AutoCalcSetting;
+
+import java.awt.Color;
+import java.awt.Container;
+import java.awt.Font;
+import java.awt.Rectangle;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Stack;
+import java.util.Vector;
/**
* DOCUMENT ME!
*
* @author $author$
- * @version $Revision$
+ * @version $Revision: 1.141 $
*/
-public class AlignViewport implements SelectionSource
+public class AlignViewport extends AlignmentViewport implements
+ SelectionSource, VamsasSource, AlignViewportI
{
- private static final int RIGHT_JUSTIFY = 1;
-
int startRes;
int endRes;
@@ -84,16 +97,6 @@ public class AlignViewport implements SelectionSource
boolean showAnnotation = true;
- boolean colourAppliesToAllGroups = true;
-
- ColourSchemeI globalColourScheme = null;
-
- boolean conservationColourSelected = false;
-
- boolean abovePIDThreshold = false;
-
- SequenceGroup selectionGroup;
-
int charHeight;
int charWidth;
@@ -106,14 +109,6 @@ public class AlignViewport implements SelectionSource
boolean seqNameItalics;
- AlignmentI alignment;
-
- ColumnSelection colSel = new ColumnSelection();
-
- int threshold;
-
- int increment;
-
NJTree currentTree = null;
boolean scaleAboveWrapped = false;
@@ -122,58 +117,28 @@ public class AlignViewport implements SelectionSource
boolean scaleRightWrapped = true;
- boolean hasHiddenColumns = false;
-
- boolean hasHiddenRows = false;
-
boolean showHiddenMarkers = true;
boolean cursorMode = false;
- // The following vector holds the features which are
- // currently visible, in the correct order or rendering
+ /**
+ * Keys are the feature types which are currently visible. Note: Values are
+ * not used!
+ */
Hashtable featuresDisplayed = null;
- /** DOCUMENT ME!! */
- public Hashtable[] hconsensus;
-
- AlignmentAnnotation consensus;
-
- AlignmentAnnotation conservation;
-
- AlignmentAnnotation quality;
-
- boolean autoCalculateConsensus = true;
-
- /** DOCUMENT ME!! */
- public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
-
- // JBPNote Prolly only need this in the applet version.
- private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
- this);
-
- boolean ignoreGapsInConsensusCalculation = false;
-
- boolean isDataset = false;
-
boolean antiAlias = false;
- boolean padGaps = false;
-
Rectangle explodedPosition;
String viewName;
- String sequenceSetID;
-
boolean gatherViewsHere = false;
Stack historyList = new Stack();
Stack redoList = new Stack();
- Hashtable sequenceColours;
-
int thresholdTextColour = 0;
Color textColour = Color.black;
@@ -182,34 +147,44 @@ public class AlignViewport implements SelectionSource
boolean rightAlignIds = false;
- Hashtable hiddenRepSequences;
-
/**
* Creates a new AlignViewport object.
*
- * @param al alignment to view
+ * @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)
+ * @param seqsetid
+ * (may be null - but potential for ambiguous constructor exception)
*/
public AlignViewport(AlignmentI al, String seqsetid)
{
- this(al,seqsetid,null);
+ 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); }
+ 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();
}
@@ -218,9 +193,9 @@ public class AlignViewport implements SelectionSource
* Create a new AlignViewport with hidden regions
*
* @param al
- * AlignmentI
+ * AlignmentI
* @param hiddenColumns
- * ColumnSelection
+ * ColumnSelection
*/
public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns)
{
@@ -228,45 +203,71 @@ public class AlignViewport implements SelectionSource
if (hiddenColumns != null)
{
this.colSel = hiddenColumns;
- if (hiddenColumns.getHiddenColumns() != null)
+ if (hiddenColumns.getHiddenColumns() != null
+ && hiddenColumns.getHiddenColumns().size() > 0)
{
hasHiddenColumns = true;
}
+ else
+ {
+ hasHiddenColumns = false;
+ }
}
init();
}
+
/**
* New viewport with hidden columns and an existing sequence set id
+ *
* @param al
* @param hiddenColumns
- * @param seqsetid (may be null)
+ * @param seqsetid
+ * (may be null)
*/
- public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns, String seqsetid)
+ public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
+ String seqsetid)
{
- this(al,hiddenColumns,seqsetid,null);
+ 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)
+ * @param seqsetid
+ * (may be null)
+ * @param viewid
+ * (may be null)
*/
- public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns, String seqsetid, String viewid)
+ 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); }
+ 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)
+ if (hiddenColumns.getHiddenColumns() != null
+ && hiddenColumns.getHiddenColumns().size() > 0)
{
hasHiddenColumns = true;
}
+ else
+ {
+ hasHiddenColumns = false;
+ }
}
init();
}
@@ -287,10 +288,10 @@ public class AlignViewport implements SelectionSource
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);
-
+ setPadGaps(Cache.getDefault("PAD_GAPS", true));
+ shownpfeats = Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true);
+ showdbrefs = Cache.getDefault("SHOW_DBREFS_TOOLTIP", true);
+
String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
String fontSize = Cache.getDefault("FONT_SIZE", "10");
@@ -319,41 +320,24 @@ public class AlignViewport implements SelectionSource
{
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);
- }
+ showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
+ showQuality = Cache.getDefault("SHOW_QUALITY", true);
+ showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
+ 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
+ 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);
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);
- }
}
-
+ initAutoAnnotation();
if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
{
globalColourScheme = ColourSchemeProperty.getColour(alignment,
@@ -373,14 +357,18 @@ public class AlignViewport implements SelectionSource
}
wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
- showUnconserved = jalview.bin.Cache.getDefault("SHOW_UNCONSERVED", 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!
+ * set the flag
*
* @param b
- * DOCUMENT ME!
+ * features are displayed if true
*/
public void setShowSequenceFeatures(boolean b)
{
@@ -392,160 +380,6 @@ public class AlignViewport implements SelectionSource
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)
- {
- new OOMWarning("calculating conservation", error);
-
- conservation = null;
- quality = null;
-
- }
-
- 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;
-
/**
* centre columnar annotation labels in displayed alignment annotation TODO:
* add to jalviewXML and annotation display settings
@@ -556,135 +390,7 @@ public class AlignViewport implements SelectionSource
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)
- {
- return;
- }
-
- conservationThread = new ConservationThread(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;
- }
- 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);
-
- for (int i = 0; i < aWidth; i++)
- {
- float value = 0;
- if (ignoreGapsInConsensusCalculation)
- {
- value = ((Float) hconsensus[i].get(AAFrequency.PID_NOGAPS))
- .floatValue();
- }
- else
- {
- value = ((Float) hconsensus[i].get(AAFrequency.PID_GAPS))
- .floatValue();
- }
-
- String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE)
- .toString();
- String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE)
- + " ";
-
- if (maxRes.length() > 1)
- {
- mouseOver = "[" + maxRes + "] ";
- maxRes = "+";
- }
-
- mouseOver += ((int) value + "%");
- consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
- value);
- }
-
- if (globalColourScheme != null)
- {
- globalColourScheme.setConsensus(hconsensus);
- }
-
- } 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);
- }
- }
- }
+ // --------END Structure Conservation
/**
* get the consensus sequence as displayed under the PID consensus annotation
@@ -729,20 +435,19 @@ public class AlignViewport implements SelectionSource
*
* @return DOCUMENT ME!
*/
- public SequenceGroup getSelectionGroup()
+ public int getStartRes()
{
- return selectionGroup;
+ return startRes;
}
/**
* DOCUMENT ME!
*
- * @param sg
- * DOCUMENT ME!
+ * @return DOCUMENT ME!
*/
- public void setSelectionGroup(SequenceGroup sg)
+ public int getEndRes()
{
- selectionGroup = sg;
+ return endRes;
}
/**
@@ -750,61 +455,75 @@ public class AlignViewport implements SelectionSource
*
* @return DOCUMENT ME!
*/
- public boolean getConservationSelected()
+ public int getStartSeq()
{
- return conservationColourSelected;
+ return startSeq;
}
/**
* DOCUMENT ME!
*
- * @param b
- * DOCUMENT ME!
+ * @param res
+ * DOCUMENT ME!
*/
- public void setConservationSelected(boolean b)
+ public void setStartRes(int res)
{
- conservationColourSelected = b;
+ this.startRes = res;
}
/**
* DOCUMENT ME!
*
- * @return DOCUMENT ME!
+ * @param seq
+ * DOCUMENT ME!
*/
- public boolean getAbovePIDThreshold()
+ public void setStartSeq(int seq)
{
- return abovePIDThreshold;
+ this.startSeq = seq;
}
/**
* DOCUMENT ME!
*
- * @param b
- * DOCUMENT ME!
+ * @param res
+ * DOCUMENT ME!
*/
- public void setAbovePIDThreshold(boolean b)
+ public void setEndRes(int res)
{
- abovePIDThreshold = b;
- }
+ if (res > (alignment.getWidth() - 1))
+ {
+ // log.System.out.println(" Corrected res from " + res + " to maximum " +
+ // (alignment.getWidth()-1));
+ res = alignment.getWidth() - 1;
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getStartRes()
- {
- return startRes;
+ if (res < 0)
+ {
+ res = 0;
+ }
+
+ this.endRes = res;
}
/**
* DOCUMENT ME!
*
- * @return DOCUMENT ME!
+ * @param seq
+ * DOCUMENT ME!
*/
- public int getEndRes()
+ public void setEndSeq(int seq)
{
- return endRes;
+ if (seq > alignment.getHeight())
+ {
+ seq = alignment.getHeight();
+ }
+
+ if (seq < 0)
+ {
+ seq = 0;
+ }
+
+ this.endSeq = seq;
}
/**
@@ -812,115 +531,18 @@ public class AlignViewport implements SelectionSource
*
* @return DOCUMENT ME!
*/
- public int getStartSeq()
+ public int getEndSeq()
{
- return startSeq;
+ return endSeq;
}
/**
* DOCUMENT ME!
*
- * @param cs
- * DOCUMENT ME!
+ * @param f
+ * 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)
+ public void setFont(Font f)
{
font = f;
@@ -946,7 +568,7 @@ public class AlignViewport implements SelectionSource
* DOCUMENT ME!
*
* @param w
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setCharWidth(int w)
{
@@ -967,7 +589,7 @@ public class AlignViewport implements SelectionSource
* DOCUMENT ME!
*
* @param h
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setCharHeight(int h)
{
@@ -988,7 +610,7 @@ public class AlignViewport implements SelectionSource
* DOCUMENT ME!
*
* @param w
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setWrappedWidth(int w)
{
@@ -1019,20 +641,20 @@ public class AlignViewport implements SelectionSource
* DOCUMENT ME!
*
* @param align
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setAlignment(AlignmentI align)
{
if (alignment != null && alignment.getCodonFrames() != null)
{
- StructureSelectionManager.getStructureSelectionManager()
- .removeMappings(alignment.getCodonFrames());
+ StructureSelectionManager.getStructureSelectionManager(
+ Desktop.instance).removeMappings(alignment.getCodonFrames());
}
this.alignment = align;
- if (alignment.getCodonFrames() != null)
+ if (alignment != null && alignment.getCodonFrames() != null)
{
- StructureSelectionManager.getStructureSelectionManager().addMappings(
- alignment.getCodonFrames());
+ StructureSelectionManager.getStructureSelectionManager(
+ Desktop.instance).addMappings(alignment.getCodonFrames());
}
}
@@ -1040,7 +662,7 @@ public class AlignViewport implements SelectionSource
* DOCUMENT ME!
*
* @param state
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setWrapAlignment(boolean state)
{
@@ -1051,7 +673,7 @@ public class AlignViewport implements SelectionSource
* DOCUMENT ME!
*
* @param state
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setShowText(boolean state)
{
@@ -1062,7 +684,7 @@ public class AlignViewport implements SelectionSource
* DOCUMENT ME!
*
* @param state
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setRenderGaps(boolean state)
{
@@ -1083,7 +705,7 @@ public class AlignViewport implements SelectionSource
* DOCUMENT ME!
*
* @param state
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setColourText(boolean state)
{
@@ -1094,7 +716,7 @@ public class AlignViewport implements SelectionSource
* DOCUMENT ME!
*
* @param state
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setShowBoxes(boolean state)
{
@@ -1145,7 +767,7 @@ public class AlignViewport implements SelectionSource
* DOCUMENT ME!
*
* @param gap
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setGapCharacter(char gap)
{
@@ -1158,48 +780,6 @@ public class AlignViewport implements SelectionSource
/**
* 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()
@@ -1211,7 +791,7 @@ public class AlignViewport implements SelectionSource
* DOCUMENT ME!
*
* @param tree
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setCurrentTree(NJTree tree)
{
@@ -1231,27 +811,6 @@ public class AlignViewport implements SelectionSource
/**
* 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()
@@ -1263,7 +822,7 @@ public class AlignViewport implements SelectionSource
* DOCUMENT ME!
*
* @param b
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setShowJVSuffix(boolean b)
{
@@ -1284,7 +843,7 @@ public class AlignViewport implements SelectionSource
* DOCUMENT ME!
*
* @param b
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setShowAnnotation(boolean b)
{
@@ -1325,7 +884,7 @@ public class AlignViewport implements SelectionSource
* DOCUMENT ME!
*
* @param b
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setScaleAboveWrapped(boolean b)
{
@@ -1336,7 +895,7 @@ public class AlignViewport implements SelectionSource
* DOCUMENT ME!
*
* @param b
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setScaleLeftWrapped(boolean b)
{
@@ -1347,69 +906,13 @@ public class AlignViewport implements SelectionSource
* DOCUMENT ME!
*
* @param b
- * DOCUMENT ME!
+ * 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;
@@ -1420,791 +923,344 @@ public class AlignViewport implements SelectionSource
return isDataset;
}
- public void hideSelectedColumns()
+ public boolean getShowHiddenMarkers()
{
- if (colSel.size() < 1)
- {
- return;
- }
-
- colSel.hideSelectedColumns();
- setSelectionGroup(null);
+ return showHiddenMarkers;
+ }
- hasHiddenColumns = true;
+ public void setShowHiddenMarkers(boolean show)
+ {
+ showHiddenMarkers = show;
}
- public void hideColumns(int start, int end)
+ /**
+ * returns the visible column regions of the alignment
+ *
+ * @param selectedRegionOnly
+ * true to just return the contigs intersecting with the selected
+ * area
+ * @return
+ */
+ public int[] getViewAsVisibleContigs(boolean selectedRegionOnly)
{
- if (start == end)
+ int[] viscontigs = null;
+ int start = 0, end = 0;
+ if (selectedRegionOnly && selectionGroup != null)
{
- colSel.hideColumns(start);
+ start = selectionGroup.getStartRes();
+ end = selectionGroup.getEndRes() + 1;
}
else
{
- colSel.hideColumns(start, end);
+ end = alignment.getWidth();
}
+ viscontigs = colSel.getVisibleContigs(start, end);
+ return viscontigs;
+ }
- hasHiddenColumns = true;
+ /**
+ * 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 new long[]
+ { -1, -1 };
+ return new long[]
+ { historyList.hashCode(), this.redoList.hashCode() };
}
- public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
+ /**
+ * 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)
{
- int sSize = sg.getSize();
- if (sSize < 2)
+ if (undoredo == null)
{
- return;
+ return true;
}
-
- if (hiddenRepSequences == null)
+ long[] cstate = getUndoRedoHash();
+ if (cstate.length != undoredo.length)
{
- 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; i < sSize; i++)
+ for (int i = 0; i < cstate.length; i++)
{
- if (sg.getSequenceAt(i) != repSequence)
+ if (cstate[i] != undoredo[i])
{
- if (index == sSize - 1)
- {
- return;
- }
-
- seqs[index++] = sg.getSequenceAt(i);
+ return true;
}
}
- sg.setSeqrep(repSequence);
- sg.setHidereps(true);
- hideSequence(seqs);
-
+ return false;
}
- public void hideAllSelectedSeqs()
+ public boolean getCentreColumnLabels()
{
- if (selectionGroup == null || selectionGroup.getSize() < 1)
- {
- return;
- }
-
- SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
-
- hideSequence(seqs);
-
- setSelectionGroup(null);
+ return centreColumnLabels;
}
- public void hideSequence(SequenceI[] seq)
+ public void setCentreColumnLabels(boolean centrecolumnlabels)
{
- if (seq != null)
- {
- for (int i = 0; i < seq.length; i++)
- {
- alignment.getHiddenSequences().hideSequence(seq[i]);
- }
- hasHiddenRows = true;
- firePropertyChange("alignment", null, alignment.getSequences());
- }
+ centreColumnLabels = centrecolumnlabels;
}
- public void showSequence(int index)
- {
- Vector tmp = alignment.getHiddenSequences().showSequence(index,
- hiddenRepSequences);
- if (tmp.size() > 0)
- {
- if (selectionGroup == null)
- {
- selectionGroup = new SequenceGroup();
- selectionGroup.setEndRes(alignment.getWidth() - 1);
- }
-
- for (int t = 0; t < tmp.size(); t++)
- {
- selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
- }
- firePropertyChange("alignment", null, alignment.getSequences());
- sendSelection();
- }
-
- if (alignment.getHiddenSequences().getSize() < 1)
- {
- hasHiddenRows = false;
- }
- }
- public void showColumn(int col)
+ /**
+ * enable or disable the display of Database Cross References in the sequence
+ * ID tooltip
+ */
+ public void setShowDbRefs(boolean show)
{
- colSel.revealHiddenColumns(col);
- if (colSel.getHiddenColumns() == null)
- {
- hasHiddenColumns = false;
- }
- }
-
- public void showAllHiddenColumns()
- {
- colSel.revealAllHiddenColumns();
- hasHiddenColumns = false;
- }
-
- public void showAllHiddenSeqs()
- {
- if (alignment.getHiddenSequences().getSize() > 0)
- {
- if (selectionGroup == null)
- {
- selectionGroup = new SequenceGroup();
- selectionGroup.setEndRes(alignment.getWidth() - 1);
- }
- Vector tmp = alignment.getHiddenSequences().showAll(
- hiddenRepSequences);
- for (int t = 0; t < tmp.size(); t++)
- {
- selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
- }
- firePropertyChange("alignment", null, alignment.getSequences());
- sendSelection();
- hasHiddenRows = false;
- hiddenRepSequences = null;
- }
- }
-
- public void invertColumnSelection()
- {
- colSel.invertColumnSelection(0, alignment.getWidth());
- }
-
- public int adjustForHiddenSeqs(int alignmentIndex)
- {
- return alignment.getHiddenSequences().adjustForHiddenSeqs(
- alignmentIndex);
+ showdbrefs = show;
}
/**
- * 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
+ * @return true if Database References are to be displayed on tooltips.
*/
- public SequenceI[] getSelectionAsNewSequence()
+ public boolean isShowDbRefs()
{
- 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;
+ return showdbrefs;
}
/**
- * get the currently selected sequence objects or all the sequences in the
- * alignment.
*
- * @return array of references to sequence objects
+ * @return true if Non-positional features are to be displayed on tooltips.
*/
- public SequenceI[] getSequenceSelection()
+ public boolean isShowNpFeats()
{
- SequenceI[] sequences;
- if (selectionGroup == null)
- {
- sequences = alignment.getSequencesArray();
- }
- else
- {
- sequences = selectionGroup.getSequencesInOrder(alignment);
- }
- return sequences;
+ return shownpfeats;
}
/**
- * 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.
+ * enable or disable the display of Non-Positional sequence features in the
+ * sequence ID tooltip
*
- * @return String[]
+ * @param show
*/
- public jalview.datamodel.CigarArray getViewAsCigars(
- boolean selectedRegionOnly)
+ public void setShowNpFeats(boolean show)
{
- CigarArray selection = null;
- SequenceI[] seqs = null;
- int i, iSize;
- int start = 0, end = 0;
- if (selectedRegionOnly && selectionGroup != null)
- {
- iSize = selectionGroup.getSize();
- seqs = selectionGroup.getSequencesInOrder(alignment);
- start = selectionGroup.getStartRes();
- end = selectionGroup.getEndRes(); // inclusive for start and end in
- // SeqCigar constructor
- }
- else
- {
- iSize = alignment.getHeight();
- seqs = alignment.getSequencesArray();
- end = alignment.getWidth() - 1;
- }
- SeqCigar[] selseqs = new SeqCigar[iSize];
- for (i = 0; i < iSize; i++)
- {
- selseqs[i] = new SeqCigar(seqs[i], start, end);
- }
- selection = new CigarArray(selseqs);
- // now construct the CigarArray operations
- if (hasHiddenColumns)
- {
- Vector regions = colSel.getHiddenColumns();
- int[] region;
- int hideStart, hideEnd;
- int last = start;
- for (int j = 0; last < end & j < regions.size(); j++)
- {
- region = (int[]) regions.elementAt(j);
- hideStart = region[0];
- hideEnd = region[1];
- // edit hidden regions to selection range
- if (hideStart < last)
- {
- if (hideEnd > last)
- {
- hideStart = last;
- }
- else
- {
- continue;
- }
- }
-
- 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);
- }
- return selection;
+ shownpfeats = show;
}
/**
- * 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);
- }
- return null;
+ * @return true if view has hidden rows
+ */
+ public boolean hasHiddenRows()
+ {
+ return hasHiddenRows;
}
/**
- * This method returns the visible alignment as text, as seen on the GUI, ie
- * if columns are hidden they will not be returned in the result. Use this for
- * calculating trees, PCA, redundancy etc on views which contain hidden
- * columns.
*
- * @return String[]
+ * @return true if view has hidden columns
*/
- 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);
- }
-
- }
- return selection;
- }
-
- public int[][] getVisibleRegionBoundaries(int min, int max)
+ public boolean hasHiddenColumns()
{
- 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;
-
+ return hasHiddenColumns;
}
- public boolean getShowHiddenMarkers()
- {
- return showHiddenMarkers;
- }
+ /**
+ * when set, view will scroll to show the highlighted position
+ */
+ public boolean followHighlight = true;
- public void setShowHiddenMarkers(boolean show)
+ /**
+ * @return true if view should scroll to show the highlighted region of a
+ * sequence
+ * @return
+ */
+ public boolean getFollowHighlight()
{
- showHiddenMarkers = show;
+ return followHighlight;
}
- public String getSequenceSetId()
- {
- if (sequenceSetID == null)
- {
- sequenceSetID = alignment.hashCode() + "";
- }
+ public boolean followSelection = true;
- return sequenceSetID;
- }
/**
- * unique viewId for synchronizing state with stored Jalview Project
- *
+ * @return true if view selection should always follow the selections
+ * broadcast by other selection sources
*/
- private String viewId=null;
-
-
- public String getViewId()
+ public boolean getFollowSelection()
{
- if (viewId==null)
- {
- viewId = this.getSequenceSetId()+"."+this.hashCode()+"";
- }
- return viewId;
+ return followSelection;
}
-
- public void alignmentChanged(AlignmentPanel ap)
- {
- if (padGaps)
- {
- alignment.padGaps();
- }
- if (hconsensus != null && autoCalculateConsensus)
- {
- updateConservation(ap);
- }
- if (autoCalculateConsensus)
- {
- updateConsensus(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();
- }
+ boolean showSeqFeaturesHeight;
- void resetAllColourSchemes()
+ public void sendSelection()
{
- ColourSchemeI cs = globalColourScheme;
- if (cs != null)
- {
- if (cs instanceof ClustalxColourScheme)
- {
- ((ClustalxColourScheme) cs).resetClustalX(alignment.getSequences(),
- alignment.getWidth());
- }
-
- cs.setConsensus(hconsensus);
- if (cs.conservationApplied())
- {
- Alignment al = (Alignment) alignment;
- Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3, al.getSequences(), 0, al
- .getWidth() - 1);
- c.calculate();
- c.verdict(false, ConsPercGaps);
-
- cs.setConservation(c);
- }
- }
-
- int s, sSize = alignment.getGroups().size();
- for (s = 0; s < sSize; s++)
- {
- 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();
- }
+ jalview.structure.StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance).sendSelection(
+ new SequenceGroup(getSelectionGroup()),
+ new ColumnSelection(getColumnSelection()), this);
}
- public Color getSequenceColour(SequenceI seq)
+ public void setShowSequenceFeaturesHeight(boolean selected)
{
- if (sequenceColours == null || !sequenceColours.containsKey(seq))
- {
- return Color.white;
- }
- else
- {
- return (Color) sequenceColours.get(seq);
- }
+ showSeqFeaturesHeight = selected;
}
- public void setSequenceColour(SequenceI seq, Color col)
+ public boolean getShowSequenceFeaturesHeight()
{
- if (sequenceColours == null)
- {
- sequenceColours = new Hashtable();
- }
-
- if (col == null)
- {
- sequenceColours.remove(seq);
- }
- else
- {
- sequenceColours.put(seq, col);
- }
+ return showSeqFeaturesHeight;
}
/**
- * returns the visible column regions of the alignment
+ * return the alignPanel containing the given viewport. Use this to get the
+ * components currently handling the given viewport.
*
- * @param selectedRegionOnly
- * true to just return the contigs intersecting with the
- * selected area
- * @return
+ * @param av
+ * @return null or an alignPanel guaranteed to have non-null alignFrame
+ * reference
*/
- public int[] getViewAsVisibleContigs(boolean selectedRegionOnly)
+ public AlignmentPanel getAlignPanel()
{
- int[] viscontigs = null;
- int start = 0, end = 0;
- if (selectedRegionOnly && selectionGroup != null)
+ AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this
+ .getSequenceSetId());
+ AlignmentPanel ap = null;
+ for (int p = 0; aps != null && p < aps.length; p++)
{
- start = selectionGroup.getStartRes();
- end = selectionGroup.getEndRes() + 1;
- }
- else
- {
- end = alignment.getWidth();
+ if (aps[p].av == this)
+ {
+ return aps[p];
+ }
}
- viscontigs = colSel.getVisibleContigs(start, end);
- return viscontigs;
+ return null;
}
- /**
- * get hash of undo and redo list for the alignment
- *
- * @return long[] { historyList.hashCode, redoList.hashCode };
- */
- public long[] getUndoRedoHash()
+ public boolean getSortByTree()
{
- if (historyList == null || redoList == null)
- return new long[]
- { -1, -1 };
- return new long[]
- { historyList.hashCode(), this.redoList.hashCode() };
+ return sortByTree;
+ }
+
+ public void setSortByTree(boolean sort)
+ {
+ sortByTree = sort;
}
/**
- * test if a particular set of hashcodes are different to the hashcodes for
- * the undo and redo list.
+ * 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 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
+ * @param sg
+ * @param wholewidth
*/
- public boolean isUndoRedoHashModified(long[] undoredo)
+ public void expandColSelection(SequenceGroup sg, boolean wholewidth)
{
- if (undoredo == null)
+ int sgs, sge;
+ if (sg != null
+ && (sgs = sg.getStartRes()) >= 0
+ && sg.getStartRes() <= (sge = sg.getEndRes())
+ && (colSel == null || colSel.getSelected() == null || colSel
+ .getSelected().size() == 0))
{
- 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])
+ if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
{
- return true;
+ // do nothing
+ return;
+ }
+ if (colSel == null)
+ {
+ colSel = new ColumnSelection();
+ }
+ for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
+ {
+ colSel.addElement(cspos);
}
}
- return false;
}
- public boolean getCentreColumnLabels()
+ public StructureSelectionManager getStructureSelectionManager()
{
- return centreColumnLabels;
+ return StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
}
- public void setCentreColumnLabels(boolean centrecolumnlabels)
- {
- centreColumnLabels = centrecolumnlabels;
- }
-
- public void updateSequenceIdColours()
+ /**
+ *
+ * @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)
{
- Vector groups = alignment.getGroups();
- if (sequenceColours == null)
+ ArrayList seqvectors = new ArrayList();
+ for (PDBEntry pdb : pdbEntries)
{
- sequenceColours = new Hashtable();
- }
- for (int ig = 0, igSize = groups.size(); ig < igSize; ig++)
- {
- SequenceGroup sg = (SequenceGroup) groups.elementAt(ig);
- if (sg.idColour != null)
+ ArrayList seqs = new ArrayList();
+ for (int i = 0; i < alignment.getHeight(); i++)
{
- Vector sqs = sg.getSequences(hiddenRepSequences);
- for (int s = 0, sSize = sqs.size(); s < sSize; s++)
+ Vector pdbs = alignment.getSequenceAt(i).getDatasetSequence()
+ .getPDBId();
+ if (pdbs == null)
+ continue;
+ SequenceI sq;
+ for (int p = 0; p < pdbs.size(); p++)
{
- sequenceColours.put(sqs.elementAt(s), sg.idColour);
+ PDBEntry p1 = (PDBEntry) pdbs.elementAt(p);
+ if (p1.getId().equals(pdb.getId()))
+ {
+ if (!seqs.contains(sq = alignment.getSequenceAt(i)))
+ seqs.add(sq);
+
+ continue;
+ }
}
}
+ seqvectors.add(seqs.toArray(new SequenceI[seqs.size()]));
}
+ return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
}
- /**
- * enable or disable the display of Database Cross References in the sequence ID tooltip
- */
- public void setShowDbRefs(boolean show)
+ public boolean isNormaliseSequenceLogo()
{
- showdbrefs=show;
+ return normaliseSequenceLogo;
}
- /**
- *
- * @return true if Database References are to be displayed on tooltips.
- */
- public boolean isShowDbRefs()
+ public void setNormaliseSequenceLogo(boolean state)
{
- return showdbrefs;
+ normaliseSequenceLogo = state;
}
/**
*
- * @return true if Non-positional features are to be displayed on tooltips.
+ * @return true if alignment characters should be displayed
*/
- public boolean isShowNpFeats()
+ public boolean isValidCharWidth()
{
- return shownpfeats;
+ return validCharWidth;
}
- /**
- * 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()
+
+ private Hashtable calcIdParams = new Hashtable();
+
+ public AutoCalcSetting getCalcIdSettingsFor(String calcId)
{
- return hasHiddenColumns;
+ return calcIdParams.get(calcId);
}
- /**
- * 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.
- * @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)
+ 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)
{
- colselhash = hc;
- return true;
+ Cache.log.debug("trigger update for " + calcId);
}
- return false;
- }
- public void sendSelection()
- {
- jalview.structure.StructureSelectionManager.getStructureSelectionManager().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;
}
}