X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=9208e5e4308cdc979b721448a9bf8c9b480f3be8;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=904e1e2d05bda4359742efa1b52566e57505cbb1;hpb=ba2255324de03f4f66ed1883c105404c4c97c66b;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 904e1e2..9208e5e 100755 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -1,1033 +1,2322 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 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 - * 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. - * - * 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 - */ -package jalview.gui; - -import jalview.analysis.*; - -import jalview.bin.*; - -import jalview.datamodel.*; - -import jalview.schemes.*; - -import java.awt.*; - -import java.util.*; - - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class AlignViewport -{ - int startRes; - int endRes; - int startSeq; - int endSeq; - boolean showFullId = false; - 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 showIdentity = true; - boolean colourAppliesToAllGroups = true; - ColourSchemeI globalColourScheme = null; - boolean conservationColourSelected = false; - boolean abovePIDThreshold = false; - SequenceGroup selectionGroup; - int charHeight; - int charWidth; - int chunkWidth; - int chunkHeight; - Font font = new Font("SansSerif", Font.PLAIN, 10); - AlignmentI alignment; - ColumnSelection colSel = new ColumnSelection(); - int threshold; - int increment; - NJTree currentTree = null; - boolean scaleAboveWrapped = false; - boolean scaleLeftWrapped = true; - boolean scaleRightWrapped = true; - - /** DOCUMENT ME!! */ - public Vector vconsensus; - AlignmentAnnotation consensus; - AlignmentAnnotation conservation; - AlignmentAnnotation quality; - - /** DOCUMENT ME!! */ - public int ConsPercGaps = 25; // JBPNote : This should be a scalable property! - - // JBPNote Prolly only need this in the applet version. - private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this); - - /** - * Creates a new AlignViewport object. - * - * @param al DOCUMENT ME! - */ - public AlignViewport(AlignmentI al) - { - setAlignment(al); - this.startRes = 0; - this.endRes = al.getWidth() - 1; - this.startSeq = 0; - this.endSeq = al.getHeight() - 1; - - updateFromPreferences(); - } - - /** - * DOCUMENT ME! - */ - public void updateFromPreferences() - { - showFullId = Preferences.showFullId; - showAnnotation = Preferences.showAnnotation; - showConservation = Preferences.showConservation; - showQuality = Preferences.showQuality; - showIdentity = Preferences.showIdentity; - showFullId = Preferences.showFullId; - - String fontName = Preferences.fontName; - String fontStyle = Preferences.fontStyle; - String fontSize = Cache.getProperty("FONT_SIZE"); - - if ((fontName != null) && (fontStyle != null) && (fontSize != null)) - { - int style = 0; - - if (fontStyle.equals("bold")) - { - style = 1; - } - else if (fontStyle.equals("italic")) - { - style = 2; - } - - setFont(new Font(fontName, style, Integer.parseInt(fontSize))); - } - else - { - setFont(font); - } - - alignment.setGapCharacter(Preferences.gapSymbol); - - // We must set conservation and consensus before setting colour, - // as Blosum and Clustal require this to be done - updateConservation(); - updateConsensus(); - - if (Preferences.defaultColour != null) - { - globalColourScheme = ColourSchemeProperty.getColour(alignment, - Preferences.defaultColour); - - if (globalColourScheme instanceof UserColourScheme) - { - globalColourScheme = UserDefinedColours.loadDefaultColours(); - } - - if (globalColourScheme != null) - { - globalColourScheme.setConsensus(vconsensus); - } - } - } - - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void showSequenceFeatures(boolean b) - { - showSequenceFeatures = b; - } - - /** - * DOCUMENT ME! - */ - public void updateConservation() - { - 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; - 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 = 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) + "", - String.valueOf(value), ' ', value, - new Color(minR + (maxR * vprop), minG + (maxG * vprop), - minB + (maxB * vprop))); - - // Quality calc - value = ((Double) cons.quality.get(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() - 1); - - if (showConservation) - { - alignment.addAnnotation(conservation); - } - - quality = new AlignmentAnnotation("Quality", - "Alignment Quality based on Blosum62 scores", qannotations, - cons.qualityRange[0].floatValue(), - cons.qualityRange[1].floatValue(), 1); - - if (showQuality) - { - alignment.addAnnotation(quality); - } - } - else - { - conservation.annotations = annotations; - quality.annotations = qannotations; - quality.graphMax = cons.qualityRange[1].floatValue(); - } - } - - /** - * DOCUMENT ME! - */ - public void updateConsensus() - { - 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) - { - vconsensus = alignment.getAAFrequency(); - } - else - { - Vector temp = alignment.getAAFrequency(); - vconsensus.clear(); - - Enumeration e = temp.elements(); - - while (e.hasMoreElements()) - { - vconsensus.add(e.nextElement()); - } - } - - Hashtable hash = null; - - for (int i = 0; i < alignment.getWidth(); i++) - { - hash = (Hashtable) vconsensus.elementAt(i); - - float value = Float.parseFloat(hash.get("maxCount").toString()); - value /= Float.parseFloat(hash.get("size").toString()); - - value *= 100; - - String maxRes = hash.get("maxResidue") + " "; - String mouseOver = hash.get("maxResidue") + " "; - - if (maxRes.length() > 2) - { - mouseOver = "[" + maxRes + "] "; - maxRes = "+ "; - } - - mouseOver += ((int) value + "%"); - annotations[i] = new Annotation(maxRes, mouseOver, ' ', value); - } - - if (consensus == null) - { - consensus = new AlignmentAnnotation("Consensus", "PID", - annotations, 0f, 100f, 1); - - if (showIdentity) - { - alignment.addAnnotation(consensus); - } - } - else - { - consensus.annotations = annotations; - } - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public SequenceGroup getSelectionGroup() - { - return selectionGroup; - } - - /** - * DOCUMENT ME! - * - * @param sg DOCUMENT ME! - */ - public void setSelectionGroup(SequenceGroup sg) - { - selectionGroup = sg; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getConservationSelected() - { - return conservationColourSelected; - } - - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setConservationSelected(boolean b) - { - conservationColourSelected = b; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getAbovePIDThreshold() - { - return abovePIDThreshold; - } - - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setAbovePIDThreshold(boolean b) - { - abovePIDThreshold = b; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getStartRes() - { - return startRes; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getEndRes() - { - return endRes; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getStartSeq() - { - return startSeq; - } - - /** - * DOCUMENT ME! - * - * @param cs DOCUMENT ME! - */ - public void setGlobalColourScheme(ColourSchemeI cs) - { - globalColourScheme = cs; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public ColourSchemeI getGlobalColourScheme() - { - return globalColourScheme; - } - - /** - * DOCUMENT ME! - * - * @param res DOCUMENT ME! - */ - public void setStartRes(int res) - { - this.startRes = res; - } - - /** - * DOCUMENT ME! - * - * @param seq DOCUMENT ME! - */ - public void setStartSeq(int seq) - { - this.startSeq = seq; - } - - /** - * DOCUMENT ME! - * - * @param res DOCUMENT ME! - */ - public void setEndRes(int res) - { - if (res > (alignment.getWidth() - 1)) - { - // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1)); - res = alignment.getWidth() - 1; - } - - if (res < 0) - { - res = 0; - } - - this.endRes = res; - } - - /** - * DOCUMENT ME! - * - * @param seq DOCUMENT ME! - */ - public void setEndSeq(int seq) - { - if (seq > alignment.getHeight()) - { - seq = alignment.getHeight(); - } - - if (seq < 0) - { - seq = 0; - } - - this.endSeq = seq; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getEndSeq() - { - return endSeq; - } - - /** - * DOCUMENT ME! - * - * @param f DOCUMENT ME! - */ - public void setFont(Font f) - { - font = f; - - Container c = new Container(); - - java.awt.FontMetrics fm = c.getFontMetrics(font); - setCharHeight(fm.getHeight()); - setCharWidth(fm.charWidth('M')); - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public Font getFont() - { - return font; - } - - /** - * DOCUMENT ME! - * - * @param w DOCUMENT ME! - */ - public void setCharWidth(int w) - { - this.charWidth = w; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getCharWidth() - { - return charWidth; - } - - /** - * DOCUMENT ME! - * - * @param h DOCUMENT ME! - */ - public void setCharHeight(int h) - { - this.charHeight = h; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getCharHeight() - { - return charHeight; - } - - /** - * DOCUMENT ME! - * - * @param w DOCUMENT ME! - */ - public void setChunkWidth(int w) - { - this.chunkWidth = w; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getChunkWidth() - { - return chunkWidth; - } - - /** - * DOCUMENT ME! - * - * @param h DOCUMENT ME! - */ - public void setChunkHeight(int h) - { - this.chunkHeight = h; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getChunkHeight() - { - return chunkHeight; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public AlignmentI getAlignment() - { - return alignment; - } - - /** - * DOCUMENT ME! - * - * @param align DOCUMENT ME! - */ - public void setAlignment(AlignmentI align) - { - this.alignment = align; - } - - /** - * DOCUMENT ME! - * - * @param state DOCUMENT ME! - */ - public void setWrapAlignment(boolean state) - { - wrapAlignment = state; - } - - /** - * DOCUMENT ME! - * - * @param state DOCUMENT ME! - */ - public void setShowText(boolean state) - { - showText = state; - } - - /** - * DOCUMENT ME! - * - * @param state DOCUMENT ME! - */ - public void setRenderGaps(boolean state) - { - renderGaps = state; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getColourText() - { - return showColourText; - } - - /** - * DOCUMENT ME! - * - * @param state DOCUMENT ME! - */ - public void setColourText(boolean state) - { - showColourText = state; - } - - /** - * DOCUMENT ME! - * - * @param state DOCUMENT ME! - */ - public void setShowBoxes(boolean state) - { - showBoxes = state; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getWrapAlignment() - { - return wrapAlignment; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getShowText() - { - return showText; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getShowBoxes() - { - return showBoxes; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public char getGapCharacter() - { - return getAlignment().getGapCharacter(); - } - - /** - * DOCUMENT ME! - * - * @param gap DOCUMENT ME! - */ - public void setGapCharacter(char gap) - { - if (getAlignment() != null) - { - getAlignment().setGapCharacter(gap); - } - } - - /** - * DOCUMENT ME! - * - * @param thresh DOCUMENT ME! - */ - public void setThreshold(int thresh) - { - threshold = thresh; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getThreshold() - { - return threshold; - } - - /** - * DOCUMENT ME! - * - * @param inc DOCUMENT ME! - */ - public void setIncrement(int inc) - { - increment = inc; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getIncrement() - { - return increment; - } - - /** - * DOCUMENT ME! - * - * @param y DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getIndex(int y) - { - int y1 = 0; - int starty = getStartSeq(); - int endy = getEndSeq(); - - for (int i = starty; i <= endy; i++) - { - if ((i < alignment.getHeight()) && - (alignment.getSequenceAt(i) != null)) - { - int y2 = y1 + getCharHeight(); - - if ((y >= y1) && (y <= y2)) - { - return i; - } - - y1 = y2; - } - else - { - return -1; - } - } - - return -1; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public ColumnSelection getColumnSelection() - { - return colSel; - } - - /** - * DOCUMENT ME! - * - * @param height DOCUMENT ME! - */ - public void resetSeqLimits(int height) - { - setEndSeq(height / getCharHeight()); - } - - /** - * DOCUMENT ME! - * - * @param tree DOCUMENT ME! - */ - public void setCurrentTree(NJTree tree) - { - currentTree = tree; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public NJTree getCurrentTree() - { - return currentTree; - } - - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setColourAppliesToAllGroups(boolean b) - { - colourAppliesToAllGroups = b; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getColourAppliesToAllGroups() - { - return colourAppliesToAllGroups; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getShowFullId() - { - return showFullId; - } - - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setShowFullId(boolean b) - { - showFullId = b; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getShowAnnotation() - { - return showAnnotation; - } - - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setShowAnnotation(boolean b) - { - showAnnotation = b; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getScaleAboveWrapped() - { - return scaleAboveWrapped; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getScaleLeftWrapped() - { - return scaleLeftWrapped; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getScaleRightWrapped() - { - return scaleRightWrapped; - } - - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setScaleAboveWrapped(boolean b) - { - scaleAboveWrapped = b; - } - - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setScaleLeftWrapped(boolean b) - { - scaleLeftWrapped = b; - } - - /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! - */ - public void setScaleRightWrapped(boolean b) - { - scaleRightWrapped = b; - } - - /** - * DOCUMENT ME! - * - * @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); - } - - /** - * DOCUMENT ME! - * - * @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); - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) + * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * + * 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. + * + * 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 . + */ +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 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 + * 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. + * + * 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 + */ +package jalview.gui; + +import java.util.*; + +import java.awt.*; + +import jalview.analysis.*; + +import jalview.bin.*; + +import jalview.datamodel.*; + +import jalview.schemes.*; +import jalview.structure.SelectionSource; +import jalview.structure.StructureSelectionManager; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class AlignViewport implements SelectionSource +{ + private static final int RIGHT_JUSTIFY = 1; + + int startRes; + + int endRes; + + int startSeq; + + int endSeq; + + 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 colourAppliesToAllGroups = true; + + ColourSchemeI globalColourScheme = null; + + boolean conservationColourSelected = false; + + boolean abovePIDThreshold = false; + + SequenceGroup selectionGroup; + + int charHeight; + + int charWidth; + + boolean validCharWidth; + + int wrappedWidth; + + Font font; + + boolean seqNameItalics; + + AlignmentI alignment; + + ColumnSelection colSel = new ColumnSelection(); + + int threshold; + + int increment; + + NJTree currentTree = null; + + boolean scaleAboveWrapped = false; + + boolean scaleLeftWrapped = true; + + boolean scaleRightWrapped = true; + + boolean hasHiddenColumns = false; + + boolean hasHiddenRows = false; + + boolean showHiddenMarkers = true; + + boolean cursorMode = false; + + /** + * Keys are the feature types which are currently visible. Note: Values are + * not used! + */ + Hashtable featuresDisplayed = null; + + /** DOCUMENT ME!! */ + public Hashtable[] hconsensus; + + AlignmentAnnotation consensus; + + AlignmentAnnotation conservation; + + AlignmentAnnotation quality; + + AlignmentAnnotation[] groupConsensus; + + AlignmentAnnotation[] groupConservation; + + boolean autoCalculateConsensus = true; + + /** DOCUMENT ME!! */ + public int ConsPercGaps = 25; // JBPNote : This should be a scalable property! + + // JBPNote Prolly only need this in the applet version. + private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport( + this); + + boolean ignoreGapsInConsensusCalculation = false; + + boolean isDataset = false; + + boolean antiAlias = false; + + boolean padGaps = false; + + Rectangle explodedPosition; + + String viewName; + + String sequenceSetID; + + boolean gatherViewsHere = false; + + Stack historyList = new Stack(); + + Stack redoList = new Stack(); + + Hashtable sequenceColours; + + int thresholdTextColour = 0; + + Color textColour = Color.black; + + Color textColour2 = Color.white; + + boolean rightAlignIds = false; + + Hashtable hiddenRepSequences; + + boolean sortByTree; + + /** + * Creates a new AlignViewport object. + * + * @param al + * alignment to view + */ + public AlignViewport(AlignmentI al) + { + setAlignment(al); + init(); + } + + /** + * Create a new AlignViewport object with a specific sequence set ID + * + * @param al + * @param seqsetid + * (may be null - but potential for ambiguous constructor exception) + */ + public AlignViewport(AlignmentI al, String seqsetid) + { + this(al, seqsetid, null); + } + + public AlignViewport(AlignmentI al, String seqsetid, String viewid) + { + sequenceSetID = seqsetid; + viewId = viewid; + // TODO remove these once 2.4.VAMSAS release finished + if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null) + { + Cache.log.debug("Setting viewport's sequence set id : " + + sequenceSetID); + } + if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null) + { + Cache.log.debug("Setting viewport's view id : " + viewId); + } + setAlignment(al); + init(); + } + + /** + * Create a new AlignViewport with hidden regions + * + * @param al + * AlignmentI + * @param hiddenColumns + * ColumnSelection + */ + public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns) + { + setAlignment(al); + if (hiddenColumns != null) + { + this.colSel = hiddenColumns; + if (hiddenColumns.getHiddenColumns() != null + && hiddenColumns.getHiddenColumns().size() > 0) + { + hasHiddenColumns = true; + } + else + { + hasHiddenColumns = false; + } + } + init(); + } + + /** + * New viewport with hidden columns and an existing sequence set id + * + * @param al + * @param hiddenColumns + * @param seqsetid + * (may be null) + */ + public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns, + String seqsetid) + { + this(al, hiddenColumns, seqsetid, null); + } + + /** + * New viewport with hidden columns and an existing sequence set id and viewid + * + * @param al + * @param hiddenColumns + * @param seqsetid + * (may be null) + * @param viewid + * (may be null) + */ + public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns, + String seqsetid, String viewid) + { + sequenceSetID = seqsetid; + viewId = viewid; + // TODO remove these once 2.4.VAMSAS release finished + if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null) + { + Cache.log.debug("Setting viewport's sequence set id : " + + sequenceSetID); + } + if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null) + { + Cache.log.debug("Setting viewport's view id : " + viewId); + } + setAlignment(al); + if (hiddenColumns != null) + { + this.colSel = hiddenColumns; + if (hiddenColumns.getHiddenColumns() != null + && hiddenColumns.getHiddenColumns().size() > 0) + { + hasHiddenColumns = true; + } + else + { + hasHiddenColumns = false; + } + } + init(); + } + + void init() + { + this.startRes = 0; + this.endRes = alignment.getWidth() - 1; + this.startSeq = 0; + this.endSeq = alignment.getHeight() - 1; + + antiAlias = Cache.getDefault("ANTI_ALIAS", false); + + showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true); + showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true); + + rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false); + centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false); + autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true); + + padGaps = Cache.getDefault("PAD_GAPS", true); + shownpfeats = Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true); + showdbrefs = Cache.getDefault("SHOW_DBREFS_TOOLTIP", true); + + String fontName = Cache.getDefault("FONT_NAME", "SansSerif"); + String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + ""); + String fontSize = Cache.getDefault("FONT_SIZE", "10"); + + seqNameItalics = Cache.getDefault("ID_ITALICS", true); + + int style = 0; + + if (fontStyle.equals("bold")) + { + style = 1; + } + else if (fontStyle.equals("italic")) + { + style = 2; + } + + setFont(new Font(fontName, style, Integer.parseInt(fontSize))); + + alignment + .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0)); + + // We must set conservation and consensus before setting colour, + // as Blosum and Clustal require this to be done + if (hconsensus == null && !isDataset) + { + if (!alignment.isNucleotide()) + { + conservation = new AlignmentAnnotation("Conservation", + "Conservation of total alignment less than " + ConsPercGaps + + "% gaps", new Annotation[1], 0f, 11f, + AlignmentAnnotation.BAR_GRAPH); + conservation.hasText = true; + conservation.autoCalculated = true; + + if (Cache.getDefault("SHOW_CONSERVATION", true)) + { + alignment.addAnnotation(conservation); + } + + if (Cache.getDefault("SHOW_QUALITY", true)) + { + quality = new AlignmentAnnotation("Quality", + "Alignment Quality based on Blosum62 scores", + new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH); + quality.hasText = true; + quality.autoCalculated = true; + + alignment.addAnnotation(quality); + } + showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION", + false); + + { + + } + } + showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", + true); + showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false); + showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false); + // TODO: add menu option action that nulls or creates consensus object + // depending on if the user wants to see the annotation or not in a + // specific alignment + consensus = new AlignmentAnnotation("Consensus", "PID", + new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); + consensus.hasText = true; + consensus.autoCalculated = true; + + if (Cache.getDefault("SHOW_IDENTITY", true)) + { + alignment.addAnnotation(consensus); + } + } + + if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null) + { + globalColourScheme = ColourSchemeProperty.getColour(alignment, + jalview.bin.Cache.getProperty("DEFAULT_COLOUR")); + + if (globalColourScheme instanceof UserColourScheme) + { + globalColourScheme = UserDefinedColours.loadDefaultColours(); + ((UserColourScheme) globalColourScheme).setThreshold(0, + getIgnoreGapsConsensus()); + } + + if (globalColourScheme != null) + { + globalColourScheme.setConsensus(hconsensus); + } + } + + wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false); + showUnconserved = jalview.bin.Cache.getDefault("SHOW_UNCONSERVED", + false); + sortByTree = jalview.bin.Cache.getDefault("SORT_BY_TREE", false); + followSelection = jalview.bin.Cache.getDefault("FOLLOW_SELECTIONS", + true); + } + + /** + * set the flag + * + * @param b + * features are displayed if true + */ + public void setShowSequenceFeatures(boolean b) + { + showSequenceFeatures = b; + } + + public boolean getShowSequenceFeatures() + { + return showSequenceFeatures; + } + + ConservationThread conservationThread; + + ConsensusThread consensusThread; + + boolean consUpdateNeeded = false; + + static boolean UPDATING_CONSENSUS = false; + + static boolean UPDATING_CONSERVATION = false; + + boolean updatingConsensus = false; + + boolean updatingConservation = false; + + /** + * centre columnar annotation labels in displayed alignment annotation TODO: + * add to jalviewXML and annotation display settings + */ + boolean centreColumnLabels = false; + + private boolean showdbrefs; + + private boolean shownpfeats; + + /** + * trigger update of conservation annotation + */ + public void updateConservation(final AlignmentPanel ap) + { + // see note in mantis : issue number 8585 + if (alignment.isNucleotide() || conservation == null + || !autoCalculateConsensus) + { + return; + } + + conservationThread = new ConservationThread(this, ap); + conservationThread.start(); + } + + /** + * trigger update of consensus annotation + */ + public void updateConsensus(final AlignmentPanel ap) + { + // see note in mantis : issue number 8585 + if (consensus == null || !autoCalculateConsensus) + { + return; + } + consensusThread = new ConsensusThread(ap); + consensusThread.start(); + } + + class ConsensusThread extends Thread + { + AlignmentPanel ap; + + public ConsensusThread(AlignmentPanel ap) + { + this.ap = ap; + } + + public void run() + { + updatingConsensus = true; + while (UPDATING_CONSENSUS) + { + try + { + if (ap != null) + { + ap.paintAlignment(false); + } + + Thread.sleep(200); + } catch (Exception ex) + { + ex.printStackTrace(); + } + } + + UPDATING_CONSENSUS = true; + + try + { + int aWidth = (alignment != null) ? alignment.getWidth() : 0; // null + // pointer + // possibility + // here. + if (aWidth < 0) + { + return; + } + + consensus.annotations = null; + consensus.annotations = new Annotation[aWidth]; + + hconsensus = new Hashtable[aWidth]; + AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment + .getWidth(), hconsensus, true); + updateAnnotation(true); + + if (globalColourScheme != null) + { + globalColourScheme.setConsensus(hconsensus); + } + + } catch (OutOfMemoryError error) + { + alignment.deleteAnnotation(consensus); + + consensus = null; + hconsensus = null; + new OOMWarning("calculating consensus", error); + } + UPDATING_CONSENSUS = false; + updatingConsensus = false; + + if (ap != null) + { + ap.paintAlignment(true); + } + } + + /** + * update the consensus annotation from the sequence profile data using + * current visualization settings. + */ + public void updateAnnotation() + { + updateAnnotation(false); + } + + protected void updateAnnotation(boolean immediate) + { + // TODO: make calls thread-safe, so if another thread calls this method, it will either return or wait until one calculation is finished. + if (immediate + || (!updatingConsensus && consensus != null && hconsensus != null)) + { + AAFrequency.completeConsensus(consensus, hconsensus, 0, + hconsensus.length, ignoreGapsInConsensusCalculation, + showSequenceLogo); + } + } + } + + /** + * 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(null); + } + 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].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" : "")); + return sq; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public SequenceGroup getSelectionGroup() + { + return selectionGroup; + } + + /** + * DOCUMENT ME! + * + * @param sg + * DOCUMENT ME! + */ + public void setSelectionGroup(SequenceGroup sg) + { + selectionGroup = sg; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getConservationSelected() + { + return conservationColourSelected; + } + + /** + * DOCUMENT ME! + * + * @param b + * DOCUMENT ME! + */ + public void setConservationSelected(boolean b) + { + conservationColourSelected = b; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getAbovePIDThreshold() + { + return abovePIDThreshold; + } + + /** + * DOCUMENT ME! + * + * @param b + * DOCUMENT ME! + */ + public void setAbovePIDThreshold(boolean b) + { + abovePIDThreshold = b; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getStartRes() + { + return startRes; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getEndRes() + { + return endRes; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getStartSeq() + { + return startSeq; + } + + /** + * DOCUMENT ME! + * + * @param cs + * DOCUMENT ME! + */ + public void setGlobalColourScheme(ColourSchemeI cs) + { + globalColourScheme = cs; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public ColourSchemeI getGlobalColourScheme() + { + return globalColourScheme; + } + + /** + * DOCUMENT ME! + * + * @param res + * DOCUMENT ME! + */ + public void setStartRes(int res) + { + this.startRes = res; + } + + /** + * DOCUMENT ME! + * + * @param seq + * DOCUMENT ME! + */ + public void setStartSeq(int seq) + { + this.startSeq = seq; + } + + /** + * DOCUMENT ME! + * + * @param res + * DOCUMENT ME! + */ + public void setEndRes(int res) + { + if (res > (alignment.getWidth() - 1)) + { + // log.System.out.println(" Corrected res from " + res + " to maximum " + + // (alignment.getWidth()-1)); + res = alignment.getWidth() - 1; + } + + if (res < 0) + { + res = 0; + } + + this.endRes = res; + } + + /** + * DOCUMENT ME! + * + * @param seq + * DOCUMENT ME! + */ + public void setEndSeq(int seq) + { + if (seq > alignment.getHeight()) + { + seq = alignment.getHeight(); + } + + if (seq < 0) + { + seq = 0; + } + + this.endSeq = seq; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getEndSeq() + { + return endSeq; + } + + /** + * DOCUMENT ME! + * + * @param f + * DOCUMENT ME! + */ + public void setFont(Font f) + { + font = f; + + Container c = new Container(); + + java.awt.FontMetrics fm = c.getFontMetrics(font); + setCharHeight(fm.getHeight()); + setCharWidth(fm.charWidth('M')); + validCharWidth = true; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public Font getFont() + { + return font; + } + + /** + * DOCUMENT ME! + * + * @param w + * DOCUMENT ME! + */ + public void setCharWidth(int w) + { + this.charWidth = w; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getCharWidth() + { + return charWidth; + } + + /** + * DOCUMENT ME! + * + * @param h + * DOCUMENT ME! + */ + public void setCharHeight(int h) + { + this.charHeight = h; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getCharHeight() + { + return charHeight; + } + + /** + * DOCUMENT ME! + * + * @param w + * DOCUMENT ME! + */ + public void setWrappedWidth(int w) + { + this.wrappedWidth = w; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getWrappedWidth() + { + return wrappedWidth; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public AlignmentI getAlignment() + { + return alignment; + } + + /** + * DOCUMENT ME! + * + * @param align + * DOCUMENT ME! + */ + public void setAlignment(AlignmentI align) + { + if (alignment != null && alignment.getCodonFrames() != null) + { + StructureSelectionManager.getStructureSelectionManager() + .removeMappings(alignment.getCodonFrames()); + } + this.alignment = align; + if (alignment.getCodonFrames() != null) + { + StructureSelectionManager.getStructureSelectionManager().addMappings( + alignment.getCodonFrames()); + } + } + + /** + * DOCUMENT ME! + * + * @param state + * DOCUMENT ME! + */ + public void setWrapAlignment(boolean state) + { + wrapAlignment = state; + } + + /** + * DOCUMENT ME! + * + * @param state + * DOCUMENT ME! + */ + public void setShowText(boolean state) + { + showText = state; + } + + /** + * DOCUMENT ME! + * + * @param state + * DOCUMENT ME! + */ + public void setRenderGaps(boolean state) + { + renderGaps = state; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getColourText() + { + return showColourText; + } + + /** + * DOCUMENT ME! + * + * @param state + * DOCUMENT ME! + */ + public void setColourText(boolean state) + { + showColourText = state; + } + + /** + * DOCUMENT ME! + * + * @param state + * DOCUMENT ME! + */ + public void setShowBoxes(boolean state) + { + showBoxes = state; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getWrapAlignment() + { + return wrapAlignment; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getShowText() + { + return showText; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getShowBoxes() + { + return showBoxes; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public char getGapCharacter() + { + return getAlignment().getGapCharacter(); + } + + /** + * DOCUMENT ME! + * + * @param gap + * DOCUMENT ME! + */ + public void setGapCharacter(char gap) + { + if (getAlignment() != null) + { + getAlignment().setGapCharacter(gap); + } + } + + /** + * DOCUMENT ME! + * + * @param thresh + * DOCUMENT ME! + */ + public void setThreshold(int thresh) + { + threshold = thresh; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getThreshold() + { + return threshold; + } + + /** + * DOCUMENT ME! + * + * @param inc + * DOCUMENT ME! + */ + public void setIncrement(int inc) + { + increment = inc; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getIncrement() + { + return increment; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public ColumnSelection getColumnSelection() + { + return colSel; + } + + /** + * DOCUMENT ME! + * + * @param tree + * DOCUMENT ME! + */ + public void setCurrentTree(NJTree tree) + { + currentTree = tree; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public NJTree getCurrentTree() + { + return currentTree; + } + + /** + * DOCUMENT ME! + * + * @param b + * DOCUMENT ME! + */ + public void setColourAppliesToAllGroups(boolean b) + { + colourAppliesToAllGroups = b; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getColourAppliesToAllGroups() + { + return colourAppliesToAllGroups; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getShowJVSuffix() + { + return showJVSuffix; + } + + /** + * DOCUMENT ME! + * + * @param b + * DOCUMENT ME! + */ + public void setShowJVSuffix(boolean b) + { + showJVSuffix = b; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getShowAnnotation() + { + return showAnnotation; + } + + /** + * DOCUMENT ME! + * + * @param b + * DOCUMENT ME! + */ + public void setShowAnnotation(boolean b) + { + showAnnotation = b; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getScaleAboveWrapped() + { + return scaleAboveWrapped; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getScaleLeftWrapped() + { + return scaleLeftWrapped; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getScaleRightWrapped() + { + return scaleRightWrapped; + } + + /** + * DOCUMENT ME! + * + * @param b + * DOCUMENT ME! + */ + public void setScaleAboveWrapped(boolean b) + { + scaleAboveWrapped = b; + } + + /** + * DOCUMENT ME! + * + * @param b + * DOCUMENT ME! + */ + public void setScaleLeftWrapped(boolean b) + { + scaleLeftWrapped = b; + } + + /** + * DOCUMENT ME! + * + * @param b + * DOCUMENT ME! + */ + public void setScaleRightWrapped(boolean b) + { + scaleRightWrapped = b; + } + + /** + * Property change listener for changes in alignment + * + * @param listener + * DOCUMENT ME! + */ + public void addPropertyChangeListener( + java.beans.PropertyChangeListener listener) + { + changeSupport.addPropertyChangeListener(listener); + } + + /** + * DOCUMENT ME! + * + * @param listener + * DOCUMENT ME! + */ + public void removePropertyChangeListener( + java.beans.PropertyChangeListener listener) + { + changeSupport.removePropertyChangeListener(listener); + } + + /** + * Property change listener for changes in alignment + * + * @param prop + * DOCUMENT ME! + * @param oldvalue + * DOCUMENT ME! + * @param newvalue + * DOCUMENT ME! + */ + public void firePropertyChange(String prop, Object oldvalue, + Object newvalue) + { + changeSupport.firePropertyChange(prop, oldvalue, newvalue); + } + + public void setIgnoreGapsConsensus(boolean b, AlignmentPanel ap) + { + ignoreGapsInConsensusCalculation = b; + updateConsensus(ap); + if (globalColourScheme != null) + { + globalColourScheme.setThreshold(globalColourScheme.getThreshold(), + ignoreGapsInConsensusCalculation); + } + } + + public boolean getIgnoreGapsConsensus() + { + return ignoreGapsInConsensusCalculation; + } + + public void setDataset(boolean b) + { + isDataset = b; + } + + public boolean isDataset() + { + return isDataset; + } + + public void hideSelectedColumns() + { + if (colSel.size() < 1) + { + return; + } + + colSel.hideSelectedColumns(); + setSelectionGroup(null); + + hasHiddenColumns = true; + } + + public void hideColumns(int start, int end) + { + if (start == end) + { + colSel.hideColumns(start); + } + else + { + colSel.hideColumns(start, end); + } + + hasHiddenColumns = true; + } + + public void hideRepSequences(SequenceI repSequence, SequenceGroup sg) + { + 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); + } + } + sg.setSeqrep(repSequence); + sg.setHidereps(true); + 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 showSequence(int index) + { + Vector tmp = alignment.getHiddenSequences().showSequence(index, + hiddenRepSequences); + if (tmp.size() > 0) + { + if (selectionGroup == null) + { + selectionGroup = new SequenceGroup(); + selectionGroup.setEndRes(alignment.getWidth() - 1); + } + + for (int t = 0; t < tmp.size(); t++) + { + selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false); + } + firePropertyChange("alignment", null, alignment.getSequences()); + sendSelection(); + } + + if (alignment.getHiddenSequences().getSize() < 1) + { + hasHiddenRows = false; + } + } + + public void showColumn(int col) + { + colSel.revealHiddenColumns(col); + if (colSel.getHiddenColumns() == null) + { + hasHiddenColumns = false; + } + } + + public void showAllHiddenColumns() + { + colSel.revealAllHiddenColumns(); + hasHiddenColumns = false; + } + + public void showAllHiddenSeqs() + { + if (alignment.getHiddenSequences().getSize() > 0) + { + if (selectionGroup == null) + { + selectionGroup = new SequenceGroup(); + selectionGroup.setEndRes(alignment.getWidth() - 1); + } + Vector tmp = alignment.getHiddenSequences().showAll( + hiddenRepSequences); + for (int t = 0; t < tmp.size(); t++) + { + selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false); + } + firePropertyChange("alignment", null, alignment.getSequences()); + sendSelection(); + hasHiddenRows = false; + hiddenRepSequences = null; + } + } + + public void invertColumnSelection() + { + colSel.invertColumnSelection(0, alignment.getWidth()); + } + + public int adjustForHiddenSeqs(int alignmentIndex) + { + return alignment.getHiddenSequences().adjustForHiddenSeqs( + alignmentIndex); + } + + /** + * This method returns an array of new SequenceI objects derived from the + * whole alignment or just the current selection with start and end points + * adjusted + * + * @note if you need references to the actual SequenceI objects in the + * alignment or currently selected then use getSequenceSelection() + * @return selection as new sequenceI objects + */ + public SequenceI[] getSelectionAsNewSequence() + { + SequenceI[] sequences; + + if (selectionGroup == null) + { + sequences = alignment.getSequencesArray(); + AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation(); + for (int i = 0; i < sequences.length; i++) + { + sequences[i] = new Sequence(sequences[i], annots); // construct new + // sequence with + // subset of visible + // annotation + } + } + else + { + sequences = selectionGroup.getSelectionAsNewSequences(alignment); + } + + return sequences; + } + + /** + * 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]; + if (hasHiddenColumns) + { + selection = colSel.getVisibleSequenceStrings(start, end, seqs); + } + else + { + for (i = 0; i < iSize; i++) + { + selection[i] = seqs[i].getSequenceAsString(start, end); + } + + } + return selection; + } + + public int[][] getVisibleRegionBoundaries(int min, int max) + { + Vector regions = new Vector(); + int start = min; + int end = max; + + do + { + if (hasHiddenColumns) + { + if (start == 0) + { + start = colSel.adjustForHiddenColumns(start); + } + + end = colSel.getHiddenBoundaryRight(start); + if (start == end) + { + end = max; + } + if (end > max) + { + end = max; + } + } + + regions.addElement(new int[] + { start, end }); + + if (hasHiddenColumns) + { + start = colSel.adjustForHiddenColumns(end); + start = colSel.getHiddenBoundaryLeft(start) + 1; + } + } while (end < max); + + int[][] startEnd = new int[regions.size()][2]; + + regions.copyInto(startEnd); + + return startEnd; + + } + + public boolean getShowHiddenMarkers() + { + return showHiddenMarkers; + } + + public void setShowHiddenMarkers(boolean show) + { + showHiddenMarkers = show; + } + + public String getSequenceSetId() + { + if (sequenceSetID == null) + { + sequenceSetID = alignment.hashCode() + ""; + } + + return sequenceSetID; + } + + /** + * unique viewId for synchronizing state with stored Jalview Project + * + */ + private String viewId = null; + + public String getViewId() + { + if (viewId == null) + { + viewId = this.getSequenceSetId() + "." + this.hashCode() + ""; + } + return viewId; + } + + public void alignmentChanged(AlignmentPanel ap) + { + if (padGaps) + { + alignment.padGaps(); + } + if (hconsensus != null && autoCalculateConsensus) + { + updateConservation(ap); + } + if (autoCalculateConsensus) + { + updateConsensus(ap); + } + + // Reset endRes of groups if beyond alignment width + int alWidth = alignment.getWidth(); + Vector groups = alignment.getGroups(); + if (groups != null) + { + for (int i = 0; i < groups.size(); i++) + { + SequenceGroup sg = (SequenceGroup) groups.elementAt(i); + if (sg.getEndRes() > alWidth) + { + sg.setEndRes(alWidth - 1); + } + } + } + + if (selectionGroup != null && selectionGroup.getEndRes() > alWidth) + { + selectionGroup.setEndRes(alWidth - 1); + } + + resetAllColourSchemes(); + + // alignment.adjustSequenceAnnotations(); + } + + 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(); + } + } + + 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); + } + } + + /** + * returns the visible column regions of the alignment + * + * @param selectedRegionOnly + * true to just return the contigs intersecting with the selected + * area + * @return + */ + public int[] getViewAsVisibleContigs(boolean selectedRegionOnly) + { + int[] viscontigs = null; + int start = 0, end = 0; + if (selectedRegionOnly && selectionGroup != null) + { + start = selectionGroup.getStartRes(); + end = selectionGroup.getEndRes() + 1; + } + else + { + end = alignment.getWidth(); + } + viscontigs = colSel.getVisibleContigs(start, end); + return viscontigs; + } + + /** + * get hash of undo and redo list for the alignment + * + * @return long[] { historyList.hashCode, redoList.hashCode }; + */ + public long[] getUndoRedoHash() + { + if (historyList == null || redoList == null) + return new long[] + { -1, -1 }; + return new long[] + { historyList.hashCode(), this.redoList.hashCode() }; + } + + /** + * test if a particular set of hashcodes are different to the hashcodes for + * the undo and redo list. + * + * @param undoredo + * the stored set of hashcodes as returned by getUndoRedoHash + * @return true if the hashcodes differ (ie the alignment has been edited) or + * the stored hashcode array differs in size + */ + public boolean isUndoRedoHashModified(long[] undoredo) + { + if (undoredo == null) + { + return true; + } + long[] cstate = getUndoRedoHash(); + if (cstate.length != undoredo.length) + { + return true; + } + + for (int i = 0; i < cstate.length; i++) + { + if (cstate[i] != undoredo[i]) + { + return true; + } + } + return false; + } + + public boolean getCentreColumnLabels() + { + return centreColumnLabels; + } + + public void setCentreColumnLabels(boolean centrecolumnlabels) + { + centreColumnLabels = centrecolumnlabels; + } + + public void updateSequenceIdColours() + { + Vector groups = alignment.getGroups(); + if (sequenceColours == null) + { + sequenceColours = new Hashtable(); + } + 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++) + { + sequenceColours.put(sqs.elementAt(s), sg.idColour); + } + } + } + } + + /** + * enable or disable the display of Database Cross References in the sequence + * ID tooltip + */ + public void setShowDbRefs(boolean show) + { + showdbrefs = show; + } + + /** + * + * @return true if Database References are to be displayed on tooltips. + */ + public boolean isShowDbRefs() + { + return showdbrefs; + } + + /** + * + * @return true if Non-positional features are to be displayed on tooltips. + */ + public boolean isShowNpFeats() + { + return shownpfeats; + } + + /** + * enable or disable the display of Non-Positional sequence features in the + * sequence ID tooltip + * + * @param show + */ + public void setShowNpFeats(boolean show) + { + shownpfeats = show; + } + + /** + * + * @return true if view has hidden rows + */ + public boolean hasHiddenRows() + { + return hasHiddenRows; + } + + /** + * + * @return true if view has hidden columns + */ + public boolean hasHiddenColumns() + { + return hasHiddenColumns; + } + + /** + * when set, view will scroll to show the highlighted position + */ + public boolean followHighlight = true; + + /** + * @return true if view should scroll to show the highlighted region of a + * sequence + * @return + */ + public boolean getFollowHighlight() + { + return followHighlight; + } + + public boolean followSelection = true; + + /** + * @return true if view selection should always follow the selections + * broadcast by other selection sources + */ + public boolean getFollowSelection() + { + return followSelection; + } + + private long sgrouphash = -1, colselhash = -1; + + boolean showSeqFeaturesHeight; + + /** + * checks current SelectionGroup against record of last hash value, and + * updates record. + * + * @return true if SelectionGroup changed since last call + */ + boolean isSelectionGroupChanged() + { + int hc = (selectionGroup == null) ? -1 : selectionGroup.hashCode(); + if (hc != sgrouphash) + { + sgrouphash = hc; + return true; + } + return false; + } + + /** + * checks current colsel against record of last hash value, and updates + * record. + * + * @return true if colsel changed since last call + */ + boolean isColSelChanged() + { + int hc = (colSel == null) ? -1 : colSel.hashCode(); + if (hc != colselhash) + { + colselhash = hc; + return true; + } + return false; + } + + public void sendSelection() + { + jalview.structure.StructureSelectionManager + .getStructureSelectionManager().sendSelection( + new SequenceGroup(getSelectionGroup()), + new ColumnSelection(getColumnSelection()), this); + } + + public void setShowSequenceFeaturesHeight(boolean selected) + { + showSeqFeaturesHeight = selected; + } + + public boolean getShowSequenceFeaturesHeight() + { + return showSeqFeaturesHeight; + } + + boolean showUnconserved = false; + + public boolean getShowUnconserved() + { + return showUnconserved; + } + + public void setShowUnconserved(boolean showunconserved) + { + showUnconserved = showunconserved; + } + + /** + * return the alignPanel containing the given viewport. Use this to get the + * components currently handling the given viewport. + * + * @param av + * @return null or an alignPanel guaranteed to have non-null alignFrame + * reference + */ + public AlignmentPanel getAlignPanel() + { + AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this + .getSequenceSetId()); + AlignmentPanel ap = null; + for (int p = 0; aps != null && p < aps.length; p++) + { + if (aps[p].av == this) + { + return aps[p]; + } + } + return null; + } + + public boolean getSortByTree() + { + return sortByTree; + } + + public void setSortByTree(boolean sort) + { + sortByTree = sort; + } + + /** + * should conservation rows be shown for groups + */ + boolean showGroupConservation = false; + + /** + * should consensus rows be shown for groups + */ + boolean showGroupConsensus = false; + + /** + * should consensus profile be rendered by default + */ + 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) + { + if (showSequenceLogo != this.showSequenceLogo) + { + // TODO: decouple settings setting from calculation when refactoring + // annotation update method from alignframe to viewport + this.showSequenceLogo = showSequenceLogo; + if (consensusThread != null) + { + consensusThread.updateAnnotation(); + } + } + this.showSequenceLogo = showSequenceLogo; + } + + /** + * @param showConsensusHistogram + * the showConsensusHistogram to set + */ + public void setShowConsensusHistogram(boolean showConsensusHistogram) + { + this.showConsensusHistogram = showConsensusHistogram; + } + + /** + * @return the showGroupConservation + */ + public boolean isShowGroupConservation() + { + return showGroupConservation; + } + + /** + * @param showGroupConservation + * the showGroupConservation to set + */ + public void setShowGroupConservation(boolean showGroupConservation) + { + this.showGroupConservation = showGroupConservation; + } + + /** + * @return the showGroupConsensus + */ + public boolean isShowGroupConsensus() + { + return showGroupConsensus; + } + + /** + * @param showGroupConsensus + * the showGroupConsensus to set + */ + public void setShowGroupConsensus(boolean showGroupConsensus) + { + this.showGroupConsensus = showGroupConsensus; + } + + /** + * + * @return flag to indicate if the consensus histogram should be rendered by + * default + */ + public boolean isShowConsensusHistogram() + { + return this.showConsensusHistogram; + } + + /** + * 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 (!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); + } + } + } +}