X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=ef17215eec78fc2d659ce594b70cee9c5a336956;hb=e2d6753e8cf3c5eaf8bccf34f4f5e9d651e9cb8e;hp=95aafab1c2056f1bc76a32d7f4aa84ae11169fd9;hpb=a822fc744dcc06e6a8d2399218da0d0dfd56cf2b;p=jalview.git
diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 95aafab..ef17215 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -1,131 +1,79 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 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.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * 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.
*/
package jalview.appletgui;
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-import jalview.api.AlignCalcManagerI;
+import jalview.analysis.NJTree;
import jalview.api.AlignViewportI;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.api.FeatureRenderer;
+import jalview.bin.JalviewLite;
+import jalview.commands.CommandI;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.UserColourScheme;
+import jalview.structure.CommandListener;
import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
import jalview.viewmodel.AlignmentViewport;
-import jalview.workers.ConservationThread;
-import jalview.workers.ConsensusThread;
-
-public class AlignViewport extends AlignmentViewport implements AlignViewportI, SelectionSource, VamsasSource
-{
- int startRes;
- int endRes;
-
- int startSeq;
-
- int endSeq;
+import java.awt.Font;
+public class AlignViewport extends AlignmentViewport implements
+ SelectionSource, VamsasSource, CommandListener
+{
boolean cursorMode = false;
- 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 showConservation = true;
-
- boolean showQuality = true;
-
- boolean showConsensus = true;
-
- boolean upperCasebold = false;
-
- boolean colourAppliesToAllGroups = true;
-
- boolean conservationColourSelected = false;
-
- boolean abovePIDThreshold = false;
-
- int charHeight;
-
- int charWidth;
-
- int wrappedWidth;
-
Font font = new Font("SansSerif", Font.PLAIN, 10);
boolean validCharWidth = true;
- int threshold;
-
- int increment;
-
NJTree currentTree = null;
- boolean scaleAboveWrapped = true;
-
- boolean scaleLeftWrapped = true;
-
- boolean scaleRightWrapped = true;
-
- // The following vector holds the features which are
- // currently visible, in the correct order or rendering
- public Hashtable featuresDisplayed;
-
-
- boolean showHiddenMarkers = true;
-
public jalview.bin.JalviewLite applet;
- Hashtable sequenceColours;
-
boolean MAC = false;
- Stack historyList = new Stack();
+ private AnnotationColumnChooser annotationColumnSelectionState;
- Stack redoList = new Stack();
-
- public void finalize() {
- applet=null;
- quality=null;
- alignment=null;
- colSel=null;
+ private FeatureRenderer featureRenderer;
+
+ public void finalize()
+ {
+ applet = null;
+ quality = null;
+ alignment = null;
+ colSel = null;
}
public AlignViewport(AlignmentI al, JalviewLite applet)
{
+ super();
calculator = new jalview.workers.AlignCalcManager();
this.applet = applet;
- setAlignment(al);
+ alignment = al;
// we always pad gaps
this.setPadGaps(true);
this.startRes = 0;
@@ -151,7 +99,7 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
+ widthScale + "). Ignoring.");
widthScale = 1;
}
- if (applet.debug)
+ if (JalviewLite.debug)
{
System.err
.println("Alignment character width scaling factor is now "
@@ -174,7 +122,7 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
+ heightScale + "). Ignoring.");
heightScale = 1;
}
- if (applet.debug)
+ if (JalviewLite.debug)
{
System.err
.println("Alignment character height scaling factor is now "
@@ -188,41 +136,56 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
if (applet != null)
{
- showJVSuffix = applet.getDefaultParameter("showFullId", showJVSuffix);
+ setShowJVSuffix(applet.getDefaultParameter("showFullId",
+ getShowJVSuffix()));
+
+ setShowAnnotation(applet.getDefaultParameter("showAnnotation",
+ isShowAnnotation()));
+
+ showConservation = applet.getDefaultParameter("showConservation",
+ showConservation);
- showAnnotation = applet.getDefaultParameter("showAnnotation", showAnnotation);
-
- showConservation = applet.getDefaultParameter("showConservation", showConservation);
-
showQuality = applet.getDefaultParameter("showQuality", showQuality);
- showConsensus = applet.getDefaultParameter("showConsensus", showConsensus);
+ showConsensus = applet.getDefaultParameter("showConsensus",
+ showConsensus);
+
+ setShowUnconserved(applet.getDefaultParameter("showUnconserved",
+ getShowUnconserved()));
- showUnconserved = applet.getDefaultParameter("showUnconserved", showUnconserved);
+ setScaleProteinAsCdna(applet.getDefaultParameter(
+ "scaleProteinAsCdna", isScaleProteinAsCdna()));
String param = applet.getParameter("upperCase");
if (param != null)
{
if (param.equalsIgnoreCase("bold"))
{
- upperCasebold = true;
+ setUpperCasebold(true);
}
}
sortByTree = applet.getDefaultParameter("sortByTree", sortByTree);
- followHighlight = applet.getDefaultParameter("automaticScrolling",followHighlight);
- followSelection = followHighlight;
+ setFollowHighlight(applet.getDefaultParameter("automaticScrolling",
+ isFollowHighlight()));
+ followSelection = isFollowHighlight();
- showSequenceLogo = applet.getDefaultParameter("showSequenceLogo", showSequenceLogo);
+ showSequenceLogo = applet.getDefaultParameter("showSequenceLogo",
+ showSequenceLogo);
- normaliseSequenceLogo = applet.getDefaultParameter("normaliseSequenceLogo", normaliseSequenceLogo);
+ normaliseSequenceLogo = applet.getDefaultParameter(
+ "normaliseSequenceLogo", applet.getDefaultParameter(
+ "normaliseLogo", normaliseSequenceLogo));
+
+ showGroupConsensus = applet.getDefaultParameter("showGroupConsensus",
+ showGroupConsensus);
+
+ showGroupConservation = applet.getDefaultParameter(
+ "showGroupConservation", showGroupConservation);
+
+ showConsensusHistogram = applet.getDefaultParameter(
+ "showConsensusHistogram", showConsensusHistogram);
- showGroupConsensus = applet.getDefaultParameter("showGroupConsensus", showGroupConsensus);
-
- showGroupConservation = applet.getDefaultParameter("showGroupConservation", showGroupConservation);
-
- showConsensusHistogram = applet.getDefaultParameter("showConsensusHistogram", showConsensusHistogram);
-
}
if (applet != null)
@@ -254,70 +217,10 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
.getParameter("userDefinedColour"));
}
}
- if (hconsensus == null)
- {
- if (!alignment.isNucleotide())
- {
- conservation = new AlignmentAnnotation("Conservation",
- "Conservation of total alignment less than " + getConsPercGaps()
- + "% gaps", new Annotation[1], 0f, 11f,
- AlignmentAnnotation.BAR_GRAPH);
- conservation.hasText = true;
- conservation.autoCalculated = true;
-
- if (showConservation)
- {
- alignment.addAnnotation(conservation);
- }
-
- if (showQuality)
- {
- 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);
- }
- } else {
- if (alignment.hasRNAStructure())
- {
- strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
- new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
- strucConsensus.hasText = true;
- strucConsensus.autoCalculated = true;
- }
- }
-
- consensus = new AlignmentAnnotation("Consensus", "PID",
- new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
- consensus.hasText = true;
- consensus.autoCalculated = true;
+ initAutoAnnotation();
- if (showConsensus)
- {
- alignment.addAnnotation(consensus);
- if (strucConsensus!=null)
- {
- alignment.addAnnotation(strucConsensus);
- }
- }
- }
-
- }
-
- public void showSequenceFeatures(boolean b)
- {
- showSequenceFeatures = b;
- }
-
- public boolean getShowSequenceFeatures()
- {
- return showSequenceFeatures;
}
-
/**
* get the consensus sequence as displayed under the PID consensus annotation
* row.
@@ -334,7 +237,7 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
{
return null;
}
- StringBuffer seqs = new StringBuffer();
+ StringBuilder seqs = new StringBuilder(consensus.annotations.length);
for (int i = 0; i < consensus.annotations.length; i++)
{
if (consensus.annotations[i] != null)
@@ -355,84 +258,6 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
return sq;
}
- public boolean getConservationSelected()
- {
- return conservationColourSelected;
- }
-
- public void setConservationSelected(boolean b)
- {
- conservationColourSelected = b;
- }
-
- public boolean getAbovePIDThreshold()
- {
- return abovePIDThreshold;
- }
-
- public void setAbovePIDThreshold(boolean b)
- {
- abovePIDThreshold = b;
- }
-
- public int getStartRes()
- {
- return startRes;
- }
-
- public int getEndRes()
- {
- return endRes;
- }
-
- public int getStartSeq()
- {
- return startSeq;
- }
-
- public void setStartRes(int res)
- {
- this.startRes = res;
- }
-
- public void setStartSeq(int seq)
- {
- this.startSeq = seq;
- }
-
- 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;
- }
-
- public void setEndSeq(int seq)
- {
- if (seq > alignment.getHeight())
- {
- seq = alignment.getHeight();
- }
- if (seq < 0)
- {
- seq = 0;
- }
- this.endSeq = seq;
- }
-
- public int getEndSeq()
- {
- return endSeq;
- }
-
java.awt.Frame nullFrame;
protected FeatureSettings featureSettings = null;
@@ -450,13 +275,13 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);
setCharHeight((int) (heightScale * fm.getHeight()));
- charWidth = (int) (widthScale * fm.charWidth('M'));
+ setCharWidth((int) (widthScale * fm.charWidth('M')));
- if (upperCasebold)
+ if (isUpperCasebold())
{
Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());
fm = nullFrame.getGraphics().getFontMetrics(f2);
- charWidth = (int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10));
+ setCharWidth((int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10)));
}
}
@@ -465,118 +290,6 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
return font;
}
- public int getCharWidth()
- {
- return charWidth;
- }
-
- public void setCharHeight(int h)
- {
- this.charHeight = h;
- }
-
- public int getCharHeight()
- {
- return charHeight;
- }
-
- public void setWrappedWidth(int w)
- {
- this.wrappedWidth = w;
- }
-
- public int getwrappedWidth()
- {
- return wrappedWidth;
- }
-
- public AlignmentI getAlignment()
- {
- return alignment;
- }
-
- public void setAlignment(AlignmentI align)
- {
- this.alignment = align;
- }
-
- public void setWrapAlignment(boolean state)
- {
- wrapAlignment = state;
- }
-
- public void setShowText(boolean state)
- {
- showText = state;
- }
-
- public void setRenderGaps(boolean state)
- {
- renderGaps = state;
- }
-
- public boolean getColourText()
- {
- return showColourText;
- }
-
- public void setColourText(boolean state)
- {
- showColourText = state;
- }
-
- public void setShowBoxes(boolean state)
- {
- showBoxes = state;
- }
-
- public boolean getWrapAlignment()
- {
- return wrapAlignment;
- }
-
- public boolean getShowText()
- {
- return showText;
- }
-
- public boolean getShowBoxes()
- {
- return showBoxes;
- }
-
- public char getGapCharacter()
- {
- return getAlignment().getGapCharacter();
- }
-
- public void setGapCharacter(char gap)
- {
- if (getAlignment() != null)
- {
- getAlignment().setGapCharacter(gap);
- }
- }
-
- public void setThreshold(int thresh)
- {
- threshold = thresh;
- }
-
- public int getThreshold()
- {
- return threshold;
- }
-
- public void setIncrement(int inc)
- {
- increment = inc;
- }
-
- public int getIncrement()
- {
- return increment;
- }
public void resetSeqLimits(int height)
{
@@ -593,120 +306,6 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
return currentTree;
}
- public void setColourAppliesToAllGroups(boolean b)
- {
- colourAppliesToAllGroups = b;
- }
-
- public boolean getColourAppliesToAllGroups()
- {
- return colourAppliesToAllGroups;
- }
-
- public boolean getShowJVSuffix()
- {
- return showJVSuffix;
- }
-
- public void setShowJVSuffix(boolean b)
- {
- showJVSuffix = b;
- }
-
- public boolean getShowAnnotation()
- {
- return showAnnotation;
- }
-
- public void setShowAnnotation(boolean b)
- {
- showAnnotation = b;
- }
-
- public boolean getScaleAboveWrapped()
- {
- return scaleAboveWrapped;
- }
-
- public boolean getScaleLeftWrapped()
- {
- return scaleLeftWrapped;
- }
-
- public boolean getScaleRightWrapped()
- {
- return scaleRightWrapped;
- }
-
- public void setScaleAboveWrapped(boolean b)
- {
- scaleAboveWrapped = b;
- }
-
- public void setScaleLeftWrapped(boolean b)
- {
- scaleLeftWrapped = b;
- }
-
- public void setScaleRightWrapped(boolean b)
- {
- scaleRightWrapped = b;
- }
-
- public void setIgnoreGapsConsensus(boolean b)
- {
- ignoreGapsInConsensusCalculation = b;
- updateConsensus(null);
- if (globalColourScheme != null)
- {
- globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
- ignoreGapsInConsensusCalculation);
-
- }
- }
-
-
-
-
-
- public boolean getShowHiddenMarkers()
- {
- return showHiddenMarkers;
- }
-
- public void setShowHiddenMarkers(boolean show)
- {
- showHiddenMarkers = show;
- }
-
- public Color getSequenceColour(SequenceI seq)
- {
- if (sequenceColours == null || !sequenceColours.containsKey(seq))
- {
- return Color.white;
- }
- else
- {
- return (Color) sequenceColours.get(seq);
- }
- }
-
- public void setSequenceColour(SequenceI seq, Color col)
- {
- if (sequenceColours == null)
- {
- sequenceColours = new Hashtable();
- }
-
- if (col == null)
- {
- sequenceColours.remove(seq);
- }
- else
- {
- sequenceColours.put(seq, col);
- }
- }
boolean centreColumnLabels;
@@ -715,30 +314,6 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
return centreColumnLabels;
}
- public void updateSequenceIdColours()
- {
- Vector groups = alignment.getGroups();
- for (int ig = 0, igSize = groups.size(); ig < igSize; ig++)
- {
- SequenceGroup sg = (SequenceGroup) groups.elementAt(ig);
- if (sg.idColour != null)
- {
- Vector sqs = sg.getSequences(getHiddenRepSequences());
- for (int s = 0, sSize = sqs.size(); s < sSize; s++)
- {
- this.setSequenceColour((SequenceI) sqs.elementAt(s), sg.idColour);
- }
- }
- }
- }
-
- public boolean followHighlight = true;
-
- public boolean getFollowHighlight()
- {
- return followHighlight;
- }
-
public boolean followSelection = true;
/**
@@ -749,16 +324,26 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
{
return followSelection;
}
+
public void sendSelection()
{
- jalview.structure.StructureSelectionManager
- .getStructureSelectionManager(applet).sendSelection(
+ getStructureSelectionManager().sendSelection(
new SequenceGroup(getSelectionGroup()),
new ColumnSelection(getColumnSelection()), this);
}
-
-
+ /**
+ * Returns an instance of the StructureSelectionManager scoped to this applet
+ * instance.
+ *
+ * @return
+ */
+ @Override
+ public StructureSelectionManager getStructureSelectionManager()
+ {
+ return jalview.structure.StructureSelectionManager
+ .getStructureSelectionManager(applet);
+ }
/**
* synthesize a column selection if none exists so it covers the given
@@ -793,12 +378,6 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
}
}
- @Override
- public boolean hasHiddenColumns()
- {
- return hasHiddenColumns;
- }
-
public boolean isNormaliseSequenceLogo()
{
return normaliseSequenceLogo;
@@ -811,11 +390,97 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
/**
*
- * @return true if alignment characters should be displayed
+ * @return true if alignment characters should be displayed
*/
public boolean isValidCharWidth()
{
return validCharWidth;
}
+ public AnnotationColumnChooser getAnnotationColumnSelectionState()
+ {
+ return annotationColumnSelectionState;
+ }
+
+ public void setAnnotationColumnSelectionState(
+ AnnotationColumnChooser annotationColumnSelectionState)
+ {
+ this.annotationColumnSelectionState = annotationColumnSelectionState;
+ }
+
+ @Override
+ public void mirrorCommand(CommandI command, boolean undo,
+ StructureSelectionManager ssm, VamsasSource source)
+ {
+ // TODO refactor so this can be pulled up to superclass or controller
+ /*
+ * Do nothing unless we are a 'complement' of the source. May replace this
+ * with direct calls not via SSM.
+ */
+ if (source instanceof AlignViewportI
+ && ((AlignViewportI) source).getCodingComplement() == this)
+ {
+ // ok to continue;
+ }
+ else
+ {
+ return;
+ }
+
+ CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(),
+ getGapCharacter());
+ if (mappedCommand != null)
+ {
+ mappedCommand.doCommand(null);
+ firePropertyChange("alignment", null, getAlignment().getSequences());
+
+ // ap.scalePanelHolder.repaint();
+ // ap.repaint();
+ }
+ }
+
+ @Override
+ public VamsasSource getVamsasSource()
+ {
+ return this;
+ }
+
+ /**
+ * If this viewport has a (Protein/cDNA) complement, then scroll the
+ * complementary alignment to match this one.
+ */
+ public void scrollComplementaryAlignment(AlignmentPanel complementPanel)
+ {
+ if (complementPanel == null)
+ {
+ return;
+ }
+
+ /*
+ * Populate a SearchResults object with the mapped location to scroll to. If
+ * there is no complement, or it is not following highlights, or no mapping
+ * is found, the result will be empty.
+ */
+ SearchResults sr = new SearchResults();
+ int seqOffset = findComplementScrollTarget(sr);
+ if (!sr.isEmpty())
+ {
+ complementPanel.setFollowingComplementScroll(true);
+ complementPanel.scrollToCentre(sr, seqOffset);
+ }
+ }
+
+ @Override
+ public FeatureRenderer getFeatureRenderer()
+ {
+ return featureRenderer;
+ }
+
+ @Override
+ public void setFeatureRenderer(FeatureRenderer featureRenderer)
+ {
+ this.featureRenderer = featureRenderer;
+
+ }
+
}