/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * 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.awt.*;
import jalview.analysis.*;
+import jalview.api.AlignViewportI;
import jalview.bin.*;
import jalview.datamodel.*;
import jalview.schemes.*;
+import jalview.structure.SelectionSource;
+import jalview.structure.VamsasSource;
+import jalview.viewmodel.AlignmentViewport;
-public class AlignViewport
+public class AlignViewport extends AlignmentViewport implements
+ AlignViewportI, SelectionSource, VamsasSource
{
int startRes;
boolean showAnnotation = true;
- boolean showConservation = true;
-
- boolean showQuality = true;
-
- boolean showConsensus = true;
-
boolean upperCasebold = false;
- boolean colourAppliesToAllGroups = true;
-
- ColourSchemeI globalColourScheme = null;
-
- boolean conservationColourSelected = false;
-
- boolean abovePIDThreshold = false;
-
- SequenceGroup selectionGroup;
-
int charHeight;
int charWidth;
boolean validCharWidth = true;
- AlignmentI alignment;
-
- ColumnSelection colSel = new ColumnSelection();
-
int threshold;
int increment;
// currently visible, in the correct order or rendering
public Hashtable featuresDisplayed;
- boolean hasHiddenColumns = false;
-
- boolean hasHiddenRows = false;
-
boolean showHiddenMarkers = true;
- public Hashtable[] hconsensus;
-
- AlignmentAnnotation consensus;
-
- AlignmentAnnotation conservation;
-
- AlignmentAnnotation quality;
-
- AlignmentAnnotation[] groupConsensus;
-
- AlignmentAnnotation[] groupConservation;
-
- boolean autocalculateConsensus = true;
-
- public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
-
- private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
- this);
-
- boolean ignoreGapsInConsensusCalculation = false;
-
- jalview.bin.JalviewLite applet;
-
- Hashtable sequenceColours;
+ public jalview.bin.JalviewLite applet;
boolean MAC = false;
Stack redoList = new Stack();
- String sequenceSetID;
-
- Hashtable hiddenRepSequences;
+ public void finalize()
+ {
+ applet = null;
+ quality = null;
+ alignment = null;
+ colSel = null;
+ }
public AlignViewport(AlignmentI al, JalviewLite applet)
{
+ calculator = new jalview.workers.AlignCalcManager();
this.applet = applet;
setAlignment(al);
+ // we always pad gaps
+ this.setPadGaps(true);
this.startRes = 0;
this.endRes = al.getWidth() - 1;
this.startSeq = 0;
if (applet != null)
{
- String param = applet.getParameter("showFullId");
- if (param != null)
- {
- showJVSuffix = Boolean.valueOf(param).booleanValue();
- }
+ showJVSuffix = applet.getDefaultParameter("showFullId", showJVSuffix);
- param = applet.getParameter("showAnnotation");
- if (param != null)
- {
- showAnnotation = Boolean.valueOf(param).booleanValue();
- }
+ showAnnotation = applet.getDefaultParameter("showAnnotation",
+ showAnnotation);
- param = applet.getParameter("showConservation");
- if (param != null)
- {
- showConservation = Boolean.valueOf(param).booleanValue();
- }
+ showConservation = applet.getDefaultParameter("showConservation",
+ showConservation);
- param = applet.getParameter("showQuality");
- if (param != null)
- {
- showQuality = Boolean.valueOf(param).booleanValue();
- }
+ showQuality = applet.getDefaultParameter("showQuality", showQuality);
- param = applet.getParameter("showConsensus");
- if (param != null)
- {
- showConsensus = Boolean.valueOf(param).booleanValue();
- }
+ showConsensus = applet.getDefaultParameter("showConsensus",
+ showConsensus);
- param = applet.getParameter("showUnconserved");
- if (param != null)
- {
- this.showUnconserved = Boolean.valueOf(param).booleanValue();
- }
+ showUnconserved = applet.getDefaultParameter("showUnconserved",
+ showUnconserved);
- param = applet.getParameter("upperCase");
+ String param = applet.getParameter("upperCase");
if (param != null)
{
if (param.equalsIgnoreCase("bold"))
upperCasebold = true;
}
}
- param = applet.getParameter("sortByTree");
- if (param != null)
- {
- sortByTree = Boolean.valueOf(param).booleanValue();
- }
+ sortByTree = applet.getDefaultParameter("sortByTree", sortByTree);
+
+ followHighlight = applet.getDefaultParameter("automaticScrolling",
+ followHighlight);
+ followSelection = followHighlight;
+
+ showSequenceLogo = applet.getDefaultParameter("showSequenceLogo",
+ showSequenceLogo);
+
+ normaliseSequenceLogo = applet.getDefaultParameter(
+ "normaliseSequenceLogo", applet.getDefaultParameter(
+ "normaliseLogo", normaliseSequenceLogo));
+
+ showGroupConsensus = applet.getDefaultParameter("showGroupConsensus",
+ showGroupConsensus);
+
+ showGroupConservation = applet.getDefaultParameter(
+ "showGroupConservation", showGroupConservation);
+
+ showConsensusHistogram = applet.getDefaultParameter(
+ "showConsensusHistogram", showConsensusHistogram);
}
.getParameter("userDefinedColour"));
}
}
- if (hconsensus == null)
- {
- 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 (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);
- }
- }
-
- consensus = new AlignmentAnnotation("Consensus", "PID",
- new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
- consensus.hasText = true;
- consensus.autoCalculated = true;
-
- if (showConsensus)
- {
- alignment.addAnnotation(consensus);
- }
- }
+ initAutoAnnotation();
}
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;
- }
- // TODO - refactor to use a graduatedColorScheme to calculate the
- // histogram colors.
- 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.elementAt(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)
- {
- System.out.println("Out of memory calculating conservation!!");
- conservation = null;
- quality = null;
- System.gc();
- }
-
- UPDATING_CONSERVATION = false;
- updatingConservation = false;
-
- if (ap != null)
- {
- ap.paintAlignment(true);
- }
-
- }
- }
-
- ConservationThread conservationThread;
-
- ConsensusThread consensusThread;
-
- boolean consUpdateNeeded = false;
-
- static boolean UPDATING_CONSENSUS = false;
-
- static boolean UPDATING_CONSERVATION = false;
-
- boolean updatingConsensus = false;
-
- boolean updatingConservation = false;
-
- /**
- * DOCUMENT ME!
- */
- public void updateConservation(final AlignmentPanel ap)
- {
- if (alignment.isNucleotide() || conservation == null)
- {
- return;
- }
-
- conservationThread = new ConservationThread(ap);
- conservationThread.start();
- }
-
- /**
- * DOCUMENT ME!
- */
- public void updateConsensus(final AlignmentPanel ap)
- {
- consensusThread = new ConsensusThread(ap);
- consensusThread.start();
- }
-
- class ConsensusThread extends Thread
- {
- AlignmentPanel ap;
-
- public ConsensusThread(AlignmentPanel ap)
- {
- this.ap = ap;
- }
-
- public void run()
- {
- updatingConsensus = true;
- while (UPDATING_CONSENSUS)
- {
- try
- {
- if (ap != null)
- {
- ap.paintAlignment(false);
- }
-
- Thread.sleep(200);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- UPDATING_CONSENSUS = true;
-
- try
- {
- int aWidth = alignment.getWidth();
- if (aWidth < 0)
- {
- return;
- }
-
- consensus.annotations = null;
- consensus.annotations = new Annotation[aWidth];
-
- hconsensus = new Hashtable[aWidth];
- AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment
- .getWidth(), hconsensus, includeAllConsensusSymbols);
- AAFrequency.completeConsensus(consensus, hconsensus, 0, aWidth,
- ignoreGapsInConsensusCalculation,
- includeAllConsensusSymbols);
-
- if (globalColourScheme != null)
- {
- globalColourScheme.setConsensus(hconsensus);
- }
-
- } catch (OutOfMemoryError error)
- {
- alignment.deleteAnnotation(consensus);
-
- consensus = null;
- hconsensus = null;
- System.out.println("Out of memory calculating consensus!!");
- System.gc();
- }
- UPDATING_CONSENSUS = false;
- updatingConsensus = false;
-
- if (ap != null)
- {
- ap.paintAlignment(true);
- }
- }
- }
-
/**
* get the consensus sequence as displayed under the PID consensus annotation
* row.
{
if (consensus == null)
{
+ updateConsensus(null);
+ }
+ if (consensus == null)
+ {
return null;
}
StringBuffer seqs = new StringBuffer();
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;
return startSeq;
}
- public void setGlobalColourScheme(ColourSchemeI cs)
- {
- globalColourScheme = cs;
- }
-
- public ColourSchemeI getGlobalColourScheme()
- {
- return globalColourScheme;
- }
-
public void setStartRes(int res)
{
this.startRes = res;
}
}
- 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()
- {
- return colSel;
- }
-
public void resetSeqLimits(int height)
{
setEndSeq(height / getCharHeight());
return currentTree;
}
- public void setColourAppliesToAllGroups(boolean b)
- {
- colourAppliesToAllGroups = b;
- }
-
- public boolean getColourAppliesToAllGroups()
- {
- return colourAppliesToAllGroups;
- }
-
public boolean getShowJVSuffix()
{
return showJVSuffix;
}
}
- /**
- * Property change listener for changes in alignment
- *
- * @param listener
- * DOCUMENT ME!
- */
- public void addPropertyChangeListener(
- java.beans.PropertyChangeListener listener)
+ public boolean getShowHiddenMarkers()
{
- changeSupport.addPropertyChangeListener(listener);
+ return showHiddenMarkers;
}
- /**
- * DOCUMENT ME!
- *
- * @param listener
- * DOCUMENT ME!
- */
- public void removePropertyChangeListener(
- java.beans.PropertyChangeListener listener)
+ public void setShowHiddenMarkers(boolean show)
{
- changeSupport.removePropertyChangeListener(listener);
+ showHiddenMarkers = show;
}
- /**
- * 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);
- }
+ boolean centreColumnLabels;
- public boolean getIgnoreGapsConsensus()
+ public boolean getCentreColumnLabels()
{
- return ignoreGapsInConsensusCalculation;
+ return centreColumnLabels;
}
- public void hideSelectedColumns()
- {
- if (colSel.size() < 1)
- {
- return;
- }
-
- colSel.hideSelectedColumns();
- setSelectionGroup(null);
-
- hasHiddenColumns = true;
- }
+ public boolean followHighlight = true;
- public void invertColumnSelection()
+ public boolean getFollowHighlight()
{
- for (int i = 0; i < alignment.getWidth(); i++)
- {
- if (colSel.contains(i))
- {
- colSel.removeElement(i);
- }
- else
- {
- if (!hasHiddenColumns || colSel.isVisible(i))
- {
- colSel.addElement(i);
- }
- }
- }
+ return followHighlight;
}
- public void hideColumns(int start, int end)
- {
- if (start == end)
- {
- colSel.hideColumns(start);
- }
- else
- {
- colSel.hideColumns(start, end);
- }
+ public boolean followSelection = true;
- hasHiddenColumns = true;
+ /**
+ * @return true if view selection should always follow the selections
+ * broadcast by other selection sources
+ */
+ public boolean getFollowSelection()
+ {
+ return followSelection;
}
- public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
+ public void sendSelection()
{
- int sSize = sg.getSize();
- if (sSize < 2)
- {
- return;
- }
-
- if (hiddenRepSequences == null)
- {
- hiddenRepSequences = new Hashtable();
- }
-
- 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++)
- {
- if (sg.getSequenceAt(i) != repSequence)
- {
- if (index == sSize - 1)
- {
- return;
- }
-
- seqs[index++] = sg.getSequenceAt(i);
- }
- }
-
- hideSequence(seqs);
-
- }
-
- public void hideAllSelectedSeqs()
- {
- if (selectionGroup == null || selectionGroup.getSize() < 1)
- {
- return;
- }
-
- SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
-
- hideSequence(seqs);
-
- setSelectionGroup(null);
- }
-
- public void hideSequence(SequenceI[] seq)
- {
- if (seq != null)
- {
- for (int i = 0; i < seq.length; i++)
- {
- alignment.getHiddenSequences().hideSequence(seq[i]);
- }
-
- hasHiddenRows = true;
- firePropertyChange("alignment", null, alignment.getSequences());
- }
- }
-
- 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)
- {
- 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());
- hasHiddenRows = false;
- hiddenRepSequences = null;
- }
- }
-
- public int adjustForHiddenSeqs(int alignmentIndex)
- {
- return alignment.getHiddenSequences().adjustForHiddenSeqs(
- alignmentIndex);
- }
-
- /**
- * This method returns the a new SequenceI [] with the selection sequence and
- * start and end points adjusted
- *
- * @return String[]
- */
- public SequenceI[] getSelectionAsNewSequence()
- {
- SequenceI[] sequences;
-
- if (selectionGroup == null)
- {
- sequences = alignment.getSequencesArray();
- }
- else
- {
- sequences = selectionGroup.getSelectionAsNewSequences(alignment);
- }
-
- return sequences;
- }
-
- /**
- * get the currently selected sequence objects or all the sequences in the
- * alignment.
- *
- * @return array of references to sequence objects
- */
- public SequenceI[] getSequenceSelection()
- {
- SequenceI[] sequences = null;
- if (selectionGroup != null)
- {
- sequences = selectionGroup.getSequencesInOrder(alignment);
- }
- if (sequences == null)
- {
- sequences = alignment.getSequencesArray();
- }
- return sequences;
- }
-
- /**
- * This method returns the visible alignment as text, as seen on the GUI, ie
- * if columns are hidden they will not be returned in the result. Use this for
- * calculating trees, PCA, redundancy etc on views which contain hidden
- * columns.
- *
- * @return String[]
- */
- public jalview.datamodel.CigarArray getViewAsCigars(
- boolean selectedRegionOnly)
- {
- 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;
- }
-
- /**
- * 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;
- }
-
- /**
- * 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)
- {
- 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];
-
- 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].getSequenceAsString(start, end);
- }
- }
-
- return selection;
- }
-
- 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);
- }
- }
-
- public String getSequenceSetId()
- {
- if (sequenceSetID == null)
- {
- sequenceSetID = alignment.hashCode() + "";
- }
-
- return sequenceSetID;
- }
-
- public void alignmentChanged(AlignmentPanel ap)
- {
- alignment.padGaps();
-
- if (hconsensus != null && autocalculateConsensus)
- {
- updateConsensus(ap);
- updateConservation(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();
-
- // AW alignment.adjustSequenceAnnotations();
- }
-
- void resetAllColourSchemes()
- {
- 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();
- }
- }
-
- boolean centreColumnLabels;
-
- public boolean getCentreColumnLabels()
- {
- 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(hiddenRepSequences);
- for (int s = 0, sSize = sqs.size(); s < sSize; s++)
- {
- this.setSequenceColour((SequenceI) sqs.elementAt(s), sg.idColour);
- }
- }
- }
- }
-
- public boolean followHighlight = false;
-
- public boolean getFollowHighlight()
- {
- return followHighlight;
- }
-
- /**
- * show non-conserved residues only
- */
- public boolean showUnconserved = false;
-
- /**
- * when set, alignment should be reordered according to a newly opened tree
- */
- public boolean sortByTree = false;
-
- /**
- * @return the showUnconserved
- */
- public boolean getShowunconserved()
- {
- return showUnconserved;
- }
-
- /**
- * @param showUnconserved
- * the showUnconserved to set
- */
- public void setShowunconserved(boolean displayNonconserved)
- {
- this.showUnconserved = displayNonconserved;
- }
-
- /**
- * consensus annotation includes all percentage for all symbols in column
- * DISABLED FOR 2.5 RELEASE (bug #60064 logo rendering is not AWT 1.1
- * compatible)
- */
- private boolean includeAllConsensusSymbols = false;
-
- /**
- * should conservation rows be shown for groups DISABLED FOR 2.5 RELEASE (bug
- * 62446)
- */
- boolean showGroupConservation = false;
-
- /**
- * should consensus rows be shown for groups DISABLED FOR 2.5 RELEASE (bug
- * 62446)
- */
- boolean showGroupConsensus = false;
-
- /**
- * should consensus profile be rendered by default DISABLED FOR 2.5 RELEASE
- * (bug #60064 logo rendering is not AWT 1.1 compatible)
- */
- public boolean showSequenceLogo = false;
-
- /**
- * should consensus histograms be rendered by default
- */
- public boolean showConsensusHistogram = true;
-
- /**
- * @return the showConsensusProfile
- */
- public boolean isShowSequenceLogo()
- {
- return showSequenceLogo;
- }
-
- /**
- * @param showSequenceLogo
- * the new value public void setShowSequenceLogo(boolean
- * showSequenceLogo) { this.showSequenceLogo = showSequenceLogo; }
- */
- /**
- * @param showGroupConsensus
- * the showGroupConsensus to set
- */
- public void setShowGroupConsensus(boolean showGroupConsensus)
- {
- this.showGroupConsensus = showGroupConsensus;
- }
-
- /**
- * @return the includeAllConsensusSymbols
- */
- public boolean isIncludeAllConsensusSymbols()
- {
- return false;
- }
-
- /**
- *
- * @return flag to indicate if the consensus histogram should be rendered by
- * default
- */
- public boolean isShowConsensusHistogram()
- {
- return this.showConsensusHistogram;
- }
+ jalview.structure.StructureSelectionManager
+ .getStructureSelectionManager(applet).sendSelection(
+ new SequenceGroup(getSelectionGroup()),
+ new ColumnSelection(getColumnSelection()), this);
+ }
/**
* synthesize a column selection if none exists so it covers the given
}
}
+ @Override
+ public boolean hasHiddenColumns()
+ {
+ return hasHiddenColumns;
+ }
+
+ public boolean isNormaliseSequenceLogo()
+ {
+ return normaliseSequenceLogo;
+ }
+
+ public void setNormaliseSequenceLogo(boolean state)
+ {
+ normaliseSequenceLogo = state;
+ }
+
+ /**
+ *
+ * @return true if alignment characters should be displayed
+ */
+ public boolean isValidCharWidth()
+ {
+ return validCharWidth;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff