/*
- * 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 2.8.2b1)
+ * 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.
- *
- * 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.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;
+
int endRes;
int startSeq;
- int endSeq;
+ 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 upperCasebold = false;
- boolean colourAppliesToAllGroups = true;
- ColourSchemeI globalColourScheme = null;
- boolean conservationColourSelected = false;
- boolean abovePIDThreshold = false;
+ boolean showAnnotation = true;
- SequenceGroup selectionGroup;
+ boolean upperCasebold = false;
int charHeight;
+
int charWidth;
+
int wrappedWidth;
Font font = new Font("SansSerif", Font.PLAIN, 10);
- boolean validCharWidth = true;
- AlignmentI alignment;
- ColumnSelection colSel = new ColumnSelection();
+ 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
+ // currently visible, in the correct order or rendering
public Hashtable featuresDisplayed;
- boolean hasHiddenColumns = false;
- boolean hasHiddenRows = false;
boolean showHiddenMarkers = true;
+ public jalview.bin.JalviewLite applet;
- public Hashtable [] hconsensus;
- AlignmentAnnotation consensus;
- AlignmentAnnotation conservation;
- AlignmentAnnotation quality;
-
- 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 MAC = false;
- boolean ignoreGapsInConsensusCalculation = false;
+ Stack historyList = new Stack();
- jalview.bin.JalviewLite applet;
+ Stack redoList = new Stack();
- boolean MAC = false;
+ 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;
this.endSeq = al.getHeight() - 1;
- setFont(font);
-
- if(System.getProperty("os.name").startsWith("Mac"))
- MAC = true;
-
if (applet != null)
{
- String param = applet.getParameter("showFullId");
+ // get the width and height scaling factors if they were specified
+ String param = applet.getParameter("widthScale");
if (param != null)
{
- showJVSuffix = 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 (applet.debug)
+ {
+ System.err
+ .println("Alignment character width scaling factor is now "
+ + widthScale);
+ }
}
-
- param = applet.getParameter("showAnnotation");
+ param = applet.getParameter("heightScale");
if (param != null)
{
- showAnnotation = 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 (applet.debug)
+ {
+ System.err
+ .println("Alignment character height scaling factor is now "
+ + heightScale);
+ }
}
+ }
+ setFont(font);
- param = applet.getParameter("showConservation");
- if (param != null)
- {
- showConservation = Boolean.valueOf(param).booleanValue();
- }
+ MAC = new jalview.util.Platform().isAMac();
- param = applet.getParameter("showQuality");
- if (param != null)
- {
- showQuality = Boolean.valueOf(param).booleanValue();
- }
+ if (applet != null)
+ {
+ showJVSuffix = applet.getDefaultParameter("showFullId", showJVSuffix);
- param = applet.getParameter("showConsensus");
- if (param != null)
- {
- showConsensus = Boolean.valueOf(param).booleanValue();
- }
+ showAnnotation = applet.getDefaultParameter("showAnnotation",
+ showAnnotation);
+
+ showConservation = applet.getDefaultParameter("showConservation",
+ showConservation);
+
+ showQuality = applet.getDefaultParameter("showQuality", showQuality);
+
+ showConsensus = applet.getDefaultParameter("showConsensus",
+ showConsensus);
+
+ showUnconserved = applet.getDefaultParameter("showUnconserved",
+ showUnconserved);
- param = applet.getParameter("upperCase");
+ String param = applet.getParameter("upperCase");
if (param != null)
{
- if(param.equalsIgnoreCase("bold"))
+ if (param.equalsIgnoreCase("bold"))
+ {
upperCasebold = true;
+ }
}
+ sortByTree = applet.getDefaultParameter("sortByTree", sortByTree);
- }
- // We must set conservation and consensus before setting colour,
- // as Blosum and Clustal require this to be done
- updateConservation();
- updateConsensus();
+ 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);
+
+ }
if (applet != null)
{
String colour = applet.getParameter("defaultColour");
- if(colour == null)
+ if (colour == null)
{
colour = applet.getParameter("userDefinedColour");
- if(colour !=null)
+ if (colour != null)
+ {
colour = "User Defined";
+ }
}
- if(colour != null)
+ if (colour != null)
{
- globalColourScheme = ColourSchemeProperty.getColour(alignment, colour);
+ globalColourScheme = ColourSchemeProperty.getColour(alignment,
+ colour);
if (globalColourScheme != null)
{
globalColourScheme.setConsensus(hconsensus);
}
}
- if(applet.getParameter("userDefinedColour")!=null)
+ if (applet.getParameter("userDefinedColour") != null)
{
- ((UserColourScheme)globalColourScheme).parseAppletParameter(
- applet.getParameter("userDefinedColour"));
+ ((UserColourScheme) globalColourScheme).parseAppletParameter(applet
+ .getParameter("userDefinedColour"));
}
-
-
}
+ initAutoAnnotation();
+
}
public void showSequenceFeatures(boolean b)
return showSequenceFeatures;
}
-
- public void updateConservation()
+ /**
+ * get the consensus sequence as displayed under the PID consensus annotation
+ * row.
+ *
+ * @return consensus sequence as a new sequence object
+ */
+ public SequenceI getConsensusSeq()
{
- if(alignment.isNucleotide())
- return;
-
- 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++)
- {
- float value = 0;
- try
- {
- value = Integer.parseInt(sequence.charAt(i) + "");
- }
- catch (Exception ex)
- {
- if (sequence.charAt(i) == '*')
- {
- value = 11;
- }
- if (sequence.charAt(i) == '+')
- {
- value = 10;
- }
- }
- 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)
- {
- alignment.addAnnotation(conservation);
- }
- quality = new AlignmentAnnotation("Quality",
- "Alignment Quality based on Blosum62 scores",
- qannotations,
- cons.qualityRange[0].floatValue(),
- cons.qualityRange[1].floatValue(),
- AlignmentAnnotation.BAR_GRAPH);
- if (showQuality)
- {
- alignment.addAnnotation(quality);
- }
- }
- else
+ if (consensus == null)
{
- conservation.annotations = annotations;
- quality.annotations = qannotations;
- quality.graphMax = cons.qualityRange[1].floatValue();
+ updateConsensus(null);
}
-
- }
-
- public void updateConsensus()
- {
- // this routine prevents vconsensus becoming a new object each time
- // consenus is calculated. Important for speed of Blosum62
- // and PID colouring of alignment
- int aWidth = alignment.getWidth();
-
- Annotation[] annotations = new Annotation[aWidth];
-
- hconsensus = new Hashtable[aWidth];
- AAFrequency.calculate(alignment.getSequencesArray(),
- 0, aWidth,
- hconsensus);
-
- for (int i = 0; i < aWidth; i++)
- {
- float value = 0;
- if(ignoreGapsInConsensusCalculation)
- value = ((Float)hconsensus[i].get("pid_nogaps")).floatValue();
- else
- value = ((Float)hconsensus[i].get("pid_gaps")).floatValue();
-
- String maxRes = hconsensus[i].get("maxResidue").toString();
- String mouseOver = hconsensus[i].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
+ StringBuffer seqs = new StringBuffer();
+ for (int i = 0; i < consensus.annotations.length; i++)
{
- consensus.annotations = annotations;
- }
-
- if(globalColourScheme!=null)
- globalColourScheme.setConsensus(hconsensus);
-
- }
- /**
- * 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));
+ }
else
+ {
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 startSeq;
}
- public void setGlobalColourScheme(ColourSchemeI cs)
- {
- globalColourScheme = cs;
- }
-
- public ColourSchemeI getGlobalColourScheme()
- {
- return globalColourScheme;
- }
-
public void setStartRes(int res)
{
this.startRes = res;
{
if (res > alignment.getWidth() - 1)
{
- // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
+ // log.System.out.println(" Corrected res from " + res + " to maximum " +
+ // (alignment.getWidth()-1));
res = alignment.getWidth() - 1;
}
if (res < 0)
}
java.awt.Frame nullFrame;
+
+ protected FeatureSettings featureSettings = null;
+
+ private float heightScale = 1, widthScale = 1;
+
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');
+ setCharHeight((int) (heightScale * fm.getHeight()));
+ charWidth = (int) (widthScale * fm.charWidth('M'));
- if(upperCasebold)
+ if (upperCasebold)
{
Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());
fm = nullFrame.getGraphics().getFontMetrics(f2);
- charWidth = fm.stringWidth("MMMMMMMMMMM") / 10;
+ charWidth = (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()
- {
- 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;
public void setIgnoreGapsConsensus(boolean b)
{
ignoreGapsInConsensusCalculation = b;
- updateConsensus();
- if (globalColourScheme!=null)
+ updateConsensus(null);
+ if (globalColourScheme != null)
{
globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
- ignoreGapsInConsensusCalculation);
+ ignoreGapsInConsensusCalculation);
}
}
- /**
- * 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)
+ public boolean getShowHiddenMarkers()
{
- changeSupport.firePropertyChange(prop, oldvalue, newvalue);
+ return showHiddenMarkers;
}
-
-
- public boolean getIgnoreGapsConsensus()
+ public void setShowHiddenMarkers(boolean show)
{
- return ignoreGapsInConsensusCalculation;
+ showHiddenMarkers = show;
}
- public void hideSelectedColumns()
- {
- if (colSel.size() < 1)
- return;
-
- colSel.hideSelectedColumns();
- setSelectionGroup(null);
- hasHiddenColumns = true;
- }
+ boolean centreColumnLabels;
- public void invertColumnSelection()
+ public boolean getCentreColumnLabels()
{
- int column;
- for (int i = 0; i < alignment.getWidth(); i++)
- {
- column = i;
-
- if (colSel.contains(column))
- colSel.removeElement(column);
- else
- colSel.addElement(column);
-
- }
+ return centreColumnLabels;
}
+ public boolean followHighlight = true;
- public void hideColumns(int start, int end)
- {
- if(start==end)
- colSel.hideColumns(start);
- else
- colSel.hideColumns(start, end);
-
- hasHiddenColumns = true;
- }
-
- public void hideAllSelectedSeqs()
+ public boolean getFollowHighlight()
{
- if (selectionGroup == null)
- return;
-
- SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
-
- hideSequence(seqs);
-
- setSelectionGroup(null);
+ return followHighlight;
}
- public void hideSequence(SequenceI [] seq)
- {
- if(seq!=null)
- {
- for (int i = 0; i < seq.length; i++)
- alignment.getHiddenSequences().hideSequence(seq[i]);
+ public boolean followSelection = true;
- hasHiddenRows = true;
- firePropertyChange("alignment", null, alignment.getSequences());
- }
- }
-
- public void showColumn(int col)
+ /**
+ * @return true if view selection should always follow the selections
+ * broadcast by other selection sources
+ */
+ public boolean getFollowSelection()
{
- colSel.revealHiddenColumns(col);
- if(colSel.getHiddenColumns()==null)
- hasHiddenColumns = false;
+ return followSelection;
}
- public void showAllHiddenColumns()
+ public void sendSelection()
{
- colSel.revealAllHiddenColumns();
- hasHiddenColumns = false;
+ jalview.structure.StructureSelectionManager
+ .getStructureSelectionManager(applet).sendSelection(
+ new SequenceGroup(getSelectionGroup()),
+ new ColumnSelection(getColumnSelection()), this);
}
- public void showAllHiddenSeqs()
- {
- if(alignment.getHiddenSequences().getSize()>0)
+ /**
+ * 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))
{
- if(selectionGroup==null)
+ if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
+ {
+ // do nothing
+ return;
+ }
+ if (colSel == null)
{
- selectionGroup = new SequenceGroup();
- selectionGroup.setEndRes(alignment.getWidth()-1);
+ colSel = new ColumnSelection();
}
- Vector tmp = alignment.getHiddenSequences().showAll();
- for(int t=0; t<tmp.size(); t++)
+ for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
{
- selectionGroup.addSequence(
- (SequenceI)tmp.elementAt(t), false
- );
+ colSel.addElement(cspos);
}
- firePropertyChange("alignment", null, alignment.getSequences());
- hasHiddenRows = false;
}
}
- public int adjustForHiddenSeqs(int alignmentIndex)
+ @Override
+ public boolean hasHiddenColumns()
{
- return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
+ return hasHiddenColumns;
}
- /**
- * This method returns the a new SequenceI [] with
- * the selection sequence and start and end points adjusted
- * @return String[]
- */
- public SequenceI[] getSelectionAsNewSequence()
+ public boolean isNormaliseSequenceLogo()
{
- SequenceI[] sequences;
-
- if (selectionGroup == null)
- sequences = alignment.getSequencesArray();
- else
- sequences = selectionGroup.getSelectionAsNewSequences(alignment);
-
- return sequences;
+ return normaliseSequenceLogo;
}
- /**
- * 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)
+ public void setNormaliseSequenceLogo(boolean state)
{
- CigarArray selection=null;
- SequenceI [] seqs= null;
- int i, iSize;
- int start = 0, end = 0;
- if(selectedRegionOnly && selectionGroup!=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);
- }
- 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;
+ normaliseSequenceLogo = state;
}
+
/**
- * 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 alignment characters should be displayed
*/
- public String [] getViewAsString(boolean selectedRegionOnly)
+ public boolean isValidCharWidth()
{
- String [] selection = null;
- SequenceI [] seqs= null;
- int i, iSize;
- int start = 0, end = 0;
- if(selectedRegionOnly && selectionGroup!=null)
- {
- iSize = selectionGroup.getSize(false);
- 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].getSequence(start, end);
- }
- }
-
- return selection;
+ return validCharWidth;
}
- public boolean getShowHiddenMarkers()
- {
- return showHiddenMarkers;
- }
-
- public void setShowHiddenMarkers(boolean show)
- {
- showHiddenMarkers = show;
- }
-
-
}
git://source.jalview.org / jalview.git / blobdiff