/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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 2.9)
+ * Copyright (C) 2015 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
package jalview.appletgui;
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-
-public class AlignViewport
+import jalview.analysis.NJTree;
+import jalview.api.AlignViewportI;
+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 java.awt.Font;
+
+public class AlignViewport extends AlignmentViewport implements
+ SelectionSource, VamsasSource, CommandListener
{
- int startRes;
- int endRes;
-
- int startSeq;
- int endSeq;
-
-
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 colourAppliesToAllGroups = true;
- ColourSchemeI globalColourScheme = null;
- boolean conservationColourSelected = false;
- boolean abovePIDThreshold = false;
-
- SequenceGroup selectionGroup;
-
- int charHeight;
- int charWidth;
- int wrappedWidth;
-
Font font = new Font("SansSerif", Font.PLAIN, 10);
- boolean validCharWidth = true;
- AlignmentI alignment;
-
- ColumnSelection colSel = new ColumnSelection();
- int threshold;
- int increment;
+ boolean validCharWidth = true;
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
- Hashtable featuresDisplayed;
-
- boolean hasHiddenColumns = false;
- boolean hasHiddenRows = false;
- boolean showHiddenMarkers = true;
-
-
- public Vector vconsensus;
- AlignmentAnnotation consensus;
- AlignmentAnnotation conservation;
- AlignmentAnnotation quality;
-
- boolean autocalculateConsensus = true;
+ public jalview.bin.JalviewLite applet;
- public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
-
- private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
-
- boolean ignoreGapsInConsensusCalculation = false;
+ boolean MAC = false;
- jalview.bin.JalviewLite applet;
+ private AnnotationColumnChooser annotationColumnSelectionState;
- boolean MAC = false;
+ 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;
this.endRes = al.getWidth() - 1;
this.startSeq = 0;
this.endSeq = al.getHeight() - 1;
- setFont(font);
-
- if(System.getProperty("os.name").startsWith("Mac"))
- MAC = true;
-
if (applet != null)
{
- String param = applet.getParameter("showFullId");
- if (param != null)
- {
- showJVSuffix = Boolean.valueOf(param).booleanValue();
- }
-
- param = applet.getParameter("showAnnotation");
+ // get the width and height scaling factors if they were specified
+ String param = applet.getParameter("widthScale");
if (param != null)
{
- showAnnotation = Boolean.valueOf(param).booleanValue();
- }
-
- param = applet.getParameter("showConservation");
- if (param != null)
- {
- showConservation = Boolean.valueOf(param).booleanValue();
- }
-
- param = applet.getParameter("showQuality");
- if (param != null)
- {
- showQuality = Boolean.valueOf(param).booleanValue();
+ try
+ {
+ widthScale = new Float(param).floatValue();
+ } catch (Exception e)
+ {
+ }
+ if (widthScale <= 1.0)
+ {
+ System.err
+ .println("Invalid alignment character width scaling factor ("
+ + widthScale + "). Ignoring.");
+ widthScale = 1;
+ }
+ if (JalviewLite.debug)
+ {
+ System.err
+ .println("Alignment character width scaling factor is now "
+ + widthScale);
+ }
}
-
- param = applet.getParameter("showConsensus");
+ param = applet.getParameter("heightScale");
if (param != null)
{
- showConsensus = Boolean.valueOf(param).booleanValue();
+ try
+ {
+ heightScale = new Float(param).floatValue();
+ } catch (Exception e)
+ {
+ }
+ if (heightScale <= 1.0)
+ {
+ System.err
+ .println("Invalid alignment character height scaling factor ("
+ + heightScale + "). Ignoring.");
+ heightScale = 1;
+ }
+ if (JalviewLite.debug)
+ {
+ System.err
+ .println("Alignment character height scaling factor is now "
+ + heightScale);
+ }
}
}
- // We must set conservation and consensus before setting colour,
- // as Blosum and Clustal require this to be done
- updateConservation();
- updateConsensus();
+ setFont(font);
+ MAC = new jalview.util.Platform().isAMac();
if (applet != null)
{
- String colour = applet.getParameter("defaultColour");
+ setShowJVSuffix(applet.getDefaultParameter("showFullId",
+ getShowJVSuffix()));
- if(colour == null)
- {
- colour = applet.getParameter("userDefinedColour");
- if(colour !=null)
- colour = "User Defined";
- }
+ setShowAnnotation(applet.getDefaultParameter("showAnnotation",
+ isShowAnnotation()));
+
+ showConservation = applet.getDefaultParameter("showConservation",
+ showConservation);
+
+ showQuality = applet.getDefaultParameter("showQuality", showQuality);
- if(colour != null)
+ showConsensus = applet.getDefaultParameter("showConsensus",
+ showConsensus);
+
+ setShowUnconserved(applet.getDefaultParameter("showUnconserved",
+ getShowUnconserved()));
+
+ setScaleProteinAsCdna(applet.getDefaultParameter(
+ "scaleProteinAsCdna", isScaleProteinAsCdna()));
+
+ String param = applet.getParameter("upperCase");
+ if (param != null)
{
- globalColourScheme = ColourSchemeProperty.getColour(alignment, colour);
- if (globalColourScheme != null)
+ if (param.equalsIgnoreCase("bold"))
{
- globalColourScheme.setConsensus(vconsensus);
+ setUpperCasebold(true);
}
}
+ sortByTree = applet.getDefaultParameter("sortByTree", sortByTree);
- if(applet.getParameter("userDefinedColour")!=null)
- {
- ((UserColourScheme)globalColourScheme).parseAppletParameter(
- applet.getParameter("userDefinedColour"));
- }
-
+ setFollowHighlight(applet.getDefaultParameter("automaticScrolling",
+ isFollowHighlight()));
+ followSelection = isFollowHighlight();
- }
- }
+ showSequenceLogo = applet.getDefaultParameter("showSequenceLogo",
+ showSequenceLogo);
- public void showSequenceFeatures(boolean b)
- {
- showSequenceFeatures = b;
- }
+ normaliseSequenceLogo = applet.getDefaultParameter(
+ "normaliseSequenceLogo", applet.getDefaultParameter(
+ "normaliseLogo", normaliseSequenceLogo));
- public boolean getShowSequenceFeatures()
- {
- return showSequenceFeatures;
- }
+ showGroupConsensus = applet.getDefaultParameter("showGroupConsensus",
+ showGroupConsensus);
+ showGroupConservation = applet.getDefaultParameter(
+ "showGroupConservation", showGroupConservation);
- public void updateConservation()
- {
- if(alignment.isNucleotide())
- return;
+ showConsensusHistogram = applet.getDefaultParameter(
+ "showConsensusHistogram", showConsensusHistogram);
- Conservation cons = new jalview.analysis.Conservation("All",
- jalview.schemes.ResidueProperties.propHash, 3,
- alignment.getSequences(), 0,
- alignment.getWidth() - 1);
- cons.calculate();
- cons.verdict(false, ConsPercGaps);
- cons.findQuality();
- int alWidth = alignment.getWidth();
- Annotation[] annotations = new Annotation[alWidth];
- Annotation[] qannotations = new Annotation[alWidth];
- String sequence = cons.getConsSequence().getSequence();
- float minR, minG, minB, maxR, maxG, 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 = cons.qualityRange[0].floatValue();
- float qmax = cons.qualityRange[1].floatValue();
+ }
- for (int i = 0; i < alWidth; i++)
+ if (applet != null)
{
- float value = 0;
- try
- {
- value = Integer.parseInt(sequence.charAt(i) + "");
- }
- catch (Exception ex)
+ String colour = applet.getParameter("defaultColour");
+
+ if (colour == null)
{
- if (sequence.charAt(i) == '*')
- {
- value = 11;
- }
- if (sequence.charAt(i) == '+')
+ colour = applet.getParameter("userDefinedColour");
+ if (colour != null)
{
- value = 10;
+ colour = "User Defined";
}
}
- float vprop = value - min;
- vprop /= max;
- annotations[i] = new Annotation(sequence.charAt(i) + "",
- "", ' ', value,
- new Color(minR + maxR * vprop,
- minG + maxG * vprop,
- minB + maxB * vprop));
- // Quality calc
- value = ( (Double) cons.quality.elementAt(i)).floatValue();
- vprop = value - qmin;
- vprop /= qmax;
- qannotations[i] = new Annotation(" ",
- String.valueOf(value), ' ', value,
- new
- Color(minR + maxR * vprop,
- minG + maxG * vprop,
- minB + maxB * vprop));
- }
-
- if (conservation == null)
- {
- conservation = new AlignmentAnnotation("Conservation",
- "Conservation of total alignment less than " +
- ConsPercGaps + "% gaps",
- annotations,
- 0f, // cons.qualityRange[0].floatValue(),
- 11f, // cons.qualityRange[1].floatValue()
- AlignmentAnnotation.BAR_GRAPH);
- if (showConservation)
+ if (colour != null)
{
- alignment.addAnnotation(conservation);
+ globalColourScheme = ColourSchemeProperty.getColour(alignment,
+ colour);
+ if (globalColourScheme != null)
+ {
+ globalColourScheme.setConsensus(hconsensus);
+ }
}
- quality = new AlignmentAnnotation("Quality",
- "Alignment Quality based on Blosum62 scores",
- qannotations,
- cons.qualityRange[0].floatValue(),
- cons.qualityRange[1].floatValue(),
- AlignmentAnnotation.BAR_GRAPH);
- if (showQuality)
+
+ if (applet.getParameter("userDefinedColour") != null)
{
- alignment.addAnnotation(quality);
+ ((UserColourScheme) globalColourScheme).parseAppletParameter(applet
+ .getParameter("userDefinedColour"));
}
}
- else
- {
- conservation.annotations = annotations;
- quality.annotations = qannotations;
- quality.graphMax = cons.qualityRange[1].floatValue();
- }
+ initAutoAnnotation();
}
- public void updateConsensus()
+ /**
+ * get the consensus sequence as displayed under the PID consensus annotation
+ * row.
+ *
+ * @return consensus sequence as a new sequence object
+ */
+ public SequenceI getConsensusSeq()
{
- Annotation[] annotations = new Annotation[alignment.getWidth()];
-
- // this routine prevents vconsensus becoming a new object each time
- // consenus is calculated. Important for speed of Blosum62
- // and PID colouring of alignment
- if (vconsensus == null)
+ if (consensus == null)
{
- vconsensus = alignment.getAAFrequency();
+ updateConsensus(null);
}
- else
- {
- Vector temp = alignment.getAAFrequency();
- vconsensus.removeAllElements();
- Enumeration e = temp.elements();
- while (e.hasMoreElements())
- {
- vconsensus.addElement(e.nextElement());
- }
- }
- Hashtable hash = null;
- for (int i = 0; i < alignment.getWidth(); i++)
- {
- hash = (Hashtable) vconsensus.elementAt(i);
- float value = 0;
- if(ignoreGapsInConsensusCalculation)
- value = ((Float)hash.get("pid_nogaps")).floatValue();
- else
- value = ((Float)hash.get("pid_gaps")).floatValue();
-
- String maxRes = hash.get("maxResidue").toString();
- String mouseOver = hash.get("maxResidue") + " ";
- if (maxRes.length() > 1)
- {
- mouseOver = "[" + maxRes + "] ";
- maxRes = "+";
- }
-
-
- mouseOver += (int) value + "%";
- annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
-
- }
-
if (consensus == null)
{
- consensus = new AlignmentAnnotation("Consensus",
- "PID", annotations, 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
- if (showConsensus)
- {
- alignment.addAnnotation(consensus);
- }
+ return null;
}
- else
+ StringBuilder seqs = new StringBuilder(consensus.annotations.length);
+ for (int i = 0; i < consensus.annotations.length; i++)
{
- consensus.annotations = annotations;
- }
-
- if(globalColourScheme!=null)
- globalColourScheme.setConsensus(vconsensus);
-
- }
- /**
- * get the consensus sequence as displayed under the PID consensus annotation row.
- * @return consensus sequence as a new sequence object
- */
- /**
- * get the consensus sequence as displayed under the PID consensus annotation row.
- * @return consensus sequence as a new sequence object
- */
- public SequenceI getConsensusSeq() {
- if (consensus==null)
- updateConsensus();
- 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] != null)
+ {
if (consensus.annotations[i].description.charAt(0) == '[')
- seqs.append(consensus.annotations[i].description.charAt(1));
+ {
+ seqs.append(consensus.annotations[i].description.charAt(1));
+ }
else
- seqs.append(consensus.annotations[i].displayCharacter);
+ {
+ seqs.append(consensus.annotations[i].displayCharacter);
+ }
}
}
SequenceI sq = new Sequence("Consensus", seqs.toString());
- sq.setDescription("Percentage Identity Consensus "+((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
+ sq.setDescription("Percentage Identity Consensus "
+ + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
return sq;
}
- public SequenceGroup getSelectionGroup()
- {
- return selectionGroup;
- }
-
- public void setSelectionGroup(SequenceGroup sg)
- {
- selectionGroup = sg;
- }
-
- 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 setGlobalColourScheme(ColourSchemeI cs)
- {
- globalColourScheme = cs;
- }
-
- public ColourSchemeI getGlobalColourScheme()
- {
- return globalColourScheme;
- }
-
- 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;
- }
+ java.awt.Frame nullFrame;
- public void setEndSeq(int seq)
- {
- if (seq > alignment.getHeight())
- {
- seq = alignment.getHeight();
- }
- if (seq < 0)
- {
- seq = 0;
- }
- this.endSeq = seq;
- }
+ protected FeatureSettings featureSettings = null;
- public int getEndSeq()
- {
- return endSeq;
- }
+ private float heightScale = 1, widthScale = 1;
- java.awt.Frame nullFrame;
public void setFont(Font f)
{
font = f;
- if(nullFrame == null)
+ if (nullFrame == null)
{
nullFrame = new java.awt.Frame();
nullFrame.addNotify();
}
java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);
- setCharHeight(fm.getHeight());
- charWidth = fm.charWidth('M');
- }
-
- public Font getFont()
- {
- return font;
- }
-
- public int getCharWidth()
- {
- return charWidth;
- }
+ setCharHeight((int) (heightScale * fm.getHeight()));
+ setCharWidth((int) (widthScale * fm.charWidth('M')));
- 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)
+ if (isUpperCasebold())
{
- getAlignment().setGapCharacter(gap);
+ Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());
+ fm = nullFrame.getGraphics().getFontMetrics(f2);
+ setCharWidth((int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10)));
}
}
- 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 setHiddenColumns(ColumnSelection colsel)
- {
- this.colSel = colsel;
- if(colSel.getHiddenColumns()!=null)
- hasHiddenColumns = true;
- }
-
- public ColumnSelection getColumnSelection()
+ public Font getFont()
{
- return colSel;
+ return font;
}
public void resetSeqLimits(int height)
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;
- }
+ boolean centreColumnLabels;
- public boolean getShowAnnotation()
+ public boolean getCentreColumnLabels()
{
- return showAnnotation;
+ return centreColumnLabels;
}
- public void setShowAnnotation(boolean b)
- {
- showAnnotation = b;
- }
-
- public boolean getScaleAboveWrapped()
- {
- return scaleAboveWrapped;
- }
-
- public boolean getScaleLeftWrapped()
- {
- return scaleLeftWrapped;
- }
-
- public boolean getScaleRightWrapped()
- {
- return scaleRightWrapped;
- }
+ public boolean followSelection = true;
- public void setScaleAboveWrapped(boolean b)
+ /**
+ * @return true if view selection should always follow the selections
+ * broadcast by other selection sources
+ */
+ public boolean getFollowSelection()
{
- scaleAboveWrapped = b;
+ return followSelection;
}
- public void setScaleLeftWrapped(boolean b)
+ public void sendSelection()
{
- scaleLeftWrapped = b;
+ getStructureSelectionManager().sendSelection(
+ new SequenceGroup(getSelectionGroup()),
+ new ColumnSelection(getColumnSelection()), this);
}
- public void setScaleRightWrapped(boolean b)
+ /**
+ * Returns an instance of the StructureSelectionManager scoped to this applet
+ * instance.
+ *
+ * @return
+ */
+ @Override
+ public StructureSelectionManager getStructureSelectionManager()
{
- scaleRightWrapped = b;
+ return jalview.structure.StructureSelectionManager
+ .getStructureSelectionManager(applet);
}
- public void setIgnoreGapsConsensus(boolean b)
- {
- ignoreGapsInConsensusCalculation = b;
- updateConsensus();
- if (globalColourScheme!=null)
+ /**
+ * synthesize a column selection if none exists so it covers the given
+ * selection group. if wholewidth is false, no column selection is made if the
+ * selection group covers the whole alignment width.
+ *
+ * @param sg
+ * @param wholewidth
+ */
+ public void expandColSelection(SequenceGroup sg, boolean wholewidth)
+ {
+ int sgs, sge;
+ if (sg != null
+ && (sgs = sg.getStartRes()) >= 0
+ && sg.getStartRes() <= (sge = sg.getEndRes())
+ && (colSel == null || colSel.getSelected() == null || colSel
+ .getSelected().size() == 0))
{
- globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
- ignoreGapsInConsensusCalculation);
-
+ if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
+ {
+ // do nothing
+ return;
+ }
+ if (colSel == null)
+ {
+ colSel = new ColumnSelection();
+ }
+ for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
+ {
+ colSel.addElement(cspos);
+ }
}
}
- /**
- * Property change listener for changes in alignment
- *
- * @param listener DOCUMENT ME!
- */
- public void addPropertyChangeListener(
- java.beans.PropertyChangeListener listener)
+ public boolean isNormaliseSequenceLogo()
{
- changeSupport.addPropertyChangeListener(listener);
+ return normaliseSequenceLogo;
}
- /**
- * DOCUMENT ME!
- *
- * @param listener DOCUMENT ME!
- */
- public void removePropertyChangeListener(
- java.beans.PropertyChangeListener listener)
+ public void setNormaliseSequenceLogo(boolean state)
{
- changeSupport.removePropertyChangeListener(listener);
+ normaliseSequenceLogo = state;
}
/**
- * Property change listener for changes in alignment
- *
- * @param prop DOCUMENT ME!
- * @param oldvalue DOCUMENT ME!
- * @param newvalue DOCUMENT ME!
+ *
+ * @return true if alignment characters should be displayed
*/
- public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
+ public boolean isValidCharWidth()
{
- changeSupport.firePropertyChange(prop, oldvalue, newvalue);
+ return validCharWidth;
}
-
-
- public boolean getIgnoreGapsConsensus()
+ public AnnotationColumnChooser getAnnotationColumnSelectionState()
{
- return ignoreGapsInConsensusCalculation;
+ return annotationColumnSelectionState;
}
- public void hideSelectedColumns()
- {
- if (colSel.size() < 1)
- return;
- colSel.hideSelectedColumns();
- setSelectionGroup(null);
-
- hasHiddenColumns = true;
+ public void setAnnotationColumnSelectionState(
+ AnnotationColumnChooser annotationColumnSelectionState)
+ {
+ this.annotationColumnSelectionState = annotationColumnSelectionState;
}
- public void invertColumnSelection()
+ @Override
+ public void mirrorCommand(CommandI command, boolean undo,
+ StructureSelectionManager ssm, VamsasSource source)
{
- int column;
- for (int i = 0; i < alignment.getWidth(); i++)
+ // 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)
{
- column = i;
-
- if (colSel.contains(column))
- colSel.removeElement(column);
- else
- colSel.addElement(column);
-
+ // ok to continue;
}
- }
-
-
- public void hideColumns(int start, int end)
- {
- if(start==end)
- colSel.hideColumns(start);
else
- colSel.hideColumns(start, end);
-
- hasHiddenColumns = true;
- }
-
- public void hideSequence(SequenceI seq)
- {
- if(seq!=null)
{
- alignment.getHiddenSequences().hideSequence(seq);
- hasHiddenRows = true;
- firePropertyChange("alignment", null, alignment.getSequences());
- }
- }
-
- public void hideAllSelectedSeqs()
- {
- if (selectionGroup == null)
return;
-
- SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
-
- for (int i = 0; i < seqs.length; i++)
- {
- alignment.getHiddenSequences().hideSequence(seqs[i]);
}
- firePropertyChange("alignment", null, alignment.getSequences());
- hasHiddenRows = true;
- setSelectionGroup(null);
- }
- public void showColumn(int col)
- {
- colSel.revealHiddenColumns(col);
- if(colSel.getHiddenColumns()==null)
- hasHiddenColumns = false;
- }
-
- public void showAllHiddenColumns()
- {
- colSel.revealAllHiddenColumns();
- hasHiddenColumns = false;
- }
-
- public void showAllHiddenSeqs()
- {
- if(alignment.getHiddenSequences().getSize()>0)
+ CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(),
+ getGapCharacter());
+ if (mappedCommand != null)
{
- if(selectionGroup==null)
- {
- selectionGroup = new SequenceGroup();
- selectionGroup.setEndRes(alignment.getWidth()-1);
- }
- Vector tmp = alignment.getHiddenSequences().showAll();
- for(int t=0; t<tmp.size(); t++)
- {
- selectionGroup.addSequence(
- (SequenceI)tmp.elementAt(t), false
- );
- }
- firePropertyChange("alignment", null, alignment.getSequences());
- hasHiddenRows = false;
- }
- }
+ mappedCommand.doCommand(null);
+ firePropertyChange("alignment", null, getAlignment().getSequences());
- public int adjustForHiddenSeqs(int alignmentIndex)
- {
- return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
+ // ap.scalePanelHolder.repaint();
+ // ap.repaint();
+ }
}
- /**
- * This method returns the a new SequenceI [] with
- * the selection sequence and start and end points adjusted
- * @return String[]
- */
- public SequenceI[] getSelectionAsNewSequence()
+ @Override
+ public VamsasSource getVamsasSource()
{
- SequenceI[] sequences;
-
- if (selectionGroup == null)
- sequences = alignment.getSequencesArray();
- else
- sequences = selectionGroup.getSelectionAsNewSequences(alignment);
-
- return sequences;
+ return this;
}
/**
- * 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[]
+ * If this viewport has a (Protein/cDNA) complement, then scroll the
+ * complementary alignment to match this one.
*/
- public jalview.datamodel.CigarArray getViewAsCigars(boolean selectedRegionOnly)
+ public void scrollComplementaryAlignment(AlignmentPanel complementPanel)
{
- CigarArray selection=null;
- SequenceI [] seqs= null;
- int i, iSize;
- int start = 0, end = 0;
- if(selectedRegionOnly && selectionGroup!=null)
+ if (complementPanel == null)
{
- iSize = selectionGroup.getSize(false);
- 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);
+ return;
}
- 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);
- } else {
- selection.addOperation(CigarArray.M, end-start);
- }
- return selection;
- }
- /**
- * return a compact representation of the current alignment selection to
- * pass to an analysis function
- * @param selectedOnly boolean true to just return the selected view
- * @return AlignmentView
- */
- jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly) {
- // JBPNote:
- // this is here because the AlignmentView constructor modifies the CigarArray
- // object. Refactoring of Cigar and alignment view representation should
- // be done to remove redundancy.
- CigarArray aligview = getViewAsCigars(selectedOnly);
- if (aligview!=null)
- return new AlignmentView(aligview);
- return null;
- }
- /**
- * This method returns the visible alignment as text, as
- * seen on the GUI, ie if columns are hidden they will not
- * be returned in the result.
- * Use this for calculating trees, PCA, redundancy etc on views
- * which contain hidden columns.
- * @return String[]
- */
- public String [] getViewAsString(boolean selectedRegionOnly)
- {
- String [] selection = null;
- SequenceI [] seqs= null;
- int i, iSize;
- int start = 0, end = 0;
- if(selectedRegionOnly && selectionGroup!=null)
+ /*
+ * 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())
{
- iSize = selectionGroup.getSize(false);
- seqs = selectionGroup.getSequencesInOrder(alignment);
- start = selectionGroup.getStartRes();
- end = selectionGroup.getEndRes()+1;
+ complementPanel.setFollowingComplementScroll(true);
+ complementPanel.scrollToCentre(sr, seqOffset);
}
- else
- {
- iSize = alignment.getHeight();
- seqs = alignment.getSequencesArray();
- end = alignment.getWidth();
- }
-
- selection = new String[iSize];
-
-
- for(i=0; i<iSize; i++)
- {
- if (hasHiddenColumns)
- {
- StringBuffer visibleSeq = new StringBuffer();
- Vector regions = colSel.getHiddenColumns();
-
- int blockStart = start, blockEnd=end;
- int [] region;
- int hideStart, hideEnd;
-
- for (int j = 0; j < regions.size(); j++)
- {
- region = (int[]) regions.elementAt(j);
- hideStart = region[0];
- hideEnd = region[1];
-
- if(hideStart < start)
- {
- continue;
- }
-
- blockStart = Math.min(blockStart, hideEnd+1);
- blockEnd = Math.min(blockEnd, hideStart);
-
- if(blockStart>blockEnd)
- {
- break;
- }
-
-
- visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
-
- blockStart = hideEnd+1;
- blockEnd = end;
- }
-
- if(end>blockStart)
- visibleSeq.append(seqs[i].getSequence(blockStart, end));
-
- selection[i] = visibleSeq.toString();
- }
- else
- {
- selection[i] = seqs[i].getSequence(start, end);
- }
- }
-
- return selection;
- }
-
- public boolean getShowHiddenMarkers()
- {
- return showHiddenMarkers;
- }
-
- public void setShowHiddenMarkers(boolean show)
- {
- showHiddenMarkers = show;
}
-
}
git://source.jalview.org / jalview.git / blobdiff