X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=14c4022098d8119ce1bd38e79ad83561b465d148;hb=0c83c631f7d7db0baad3335805c15dd40c0aed59;hp=35a87d49da4d4218197641337c0458815977e160;hpb=8e1be43e250107a4d86898bd554cf03098fa5957;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 35a87d4..14c4022 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -22,7 +22,7 @@ package jalview.gui; import jalview.analysis.AlignmentUtils; import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; -import jalview.analysis.NJTree; +import jalview.analysis.TreeModel; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.api.FeatureColourI; @@ -35,17 +35,17 @@ import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.PDBEntry; import jalview.datamodel.SearchResults; import jalview.datamodel.SearchResultsI; -import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; -import jalview.schemes.CollectionColourScheme; +import jalview.renderer.ResidueShader; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemeProperty; +import jalview.schemes.ResidueColourScheme; import jalview.schemes.UserColourScheme; -import jalview.structure.CommandListener; import jalview.structure.SelectionSource; import jalview.structure.StructureSelectionManager; import jalview.structure.VamsasSource; @@ -56,9 +56,11 @@ import jalview.ws.params.AutoCalcSetting; import java.awt.Container; import java.awt.Dimension; import java.awt.Font; +import java.awt.FontMetrics; import java.awt.Rectangle; import java.util.ArrayList; import java.util.Hashtable; +import java.util.Iterator; import java.util.List; import java.util.Vector; @@ -70,13 +72,11 @@ import javax.swing.JInternalFrame; * @author $author$ * @version $Revision: 1.141 $ */ -public class AlignViewport extends AlignmentViewport implements - SelectionSource, CommandListener +public class AlignViewport extends AlignmentViewport + implements SelectionSource { Font font; - NJTree currentTree = null; - boolean cursorMode = false; boolean antiAlias = false; @@ -104,7 +104,7 @@ public class AlignViewport extends AlignmentViewport implements */ public AlignViewport(AlignmentI al) { - setAlignment(al); + super(al); init(); } @@ -122,20 +122,21 @@ public class AlignViewport extends AlignmentViewport implements public AlignViewport(AlignmentI al, String seqsetid, String viewid) { + super(al); 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); + 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(); + } /** @@ -146,12 +147,12 @@ public class AlignViewport extends AlignmentViewport implements * @param hiddenColumns * ColumnSelection */ - public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns) + public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns) { - setAlignment(al); + super(al); if (hiddenColumns != null) { - colSel = hiddenColumns; + al.setHiddenColumns(hiddenColumns); } init(); } @@ -164,7 +165,7 @@ public class AlignViewport extends AlignmentViewport implements * @param seqsetid * (may be null) */ - public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns, + public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns, String seqsetid) { this(al, hiddenColumns, seqsetid, null); @@ -180,25 +181,26 @@ public class AlignViewport extends AlignmentViewport implements * @param viewid * (may be null) */ - public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns, + public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns, String seqsetid, String viewid) { + super(al); 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); + 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) { - colSel = hiddenColumns; + al.setHiddenColumns(hiddenColumns); } init(); } @@ -222,25 +224,21 @@ public class AlignViewport extends AlignmentViewport implements setShowDBRefs(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true)); viewStyle.setSeqNameItalics(Cache.getDefault("ID_ITALICS", true)); viewStyle.setWrapAlignment(Cache.getDefault("WRAP_ALIGNMENT", false)); - viewStyle.setShowUnconserved(Cache - .getDefault("SHOW_UNCONSERVED", false)); + viewStyle.setShowUnconserved( + Cache.getDefault("SHOW_UNCONSERVED", false)); sortByTree = Cache.getDefault("SORT_BY_TREE", false); followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true); - sortAnnotationsBy = SequenceAnnotationOrder.valueOf(Cache.getDefault( - Preferences.SORT_ANNOTATIONS, - SequenceAnnotationOrder.NONE.name())); - showAutocalculatedAbove = Cache.getDefault( - Preferences.SHOW_AUTOCALC_ABOVE, false); - viewStyle.setScaleProteinAsCdna(Cache.getDefault( - Preferences.SCALE_PROTEIN_TO_CDNA, true)); + sortAnnotationsBy = SequenceAnnotationOrder + .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS, + SequenceAnnotationOrder.NONE.name())); + showAutocalculatedAbove = Cache + .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false); + viewStyle.setScaleProteinAsCdna( + Cache.getDefault(Preferences.SCALE_PROTEIN_TO_CDNA, true)); } void init() { - this.startRes = 0; - this.endRes = alignment.getWidth() - 1; - this.startSeq = 0; - this.endSeq = alignment.getHeight() - 1; applyViewProperties(); String fontName = Cache.getDefault("FONT_NAME", "SansSerif"); @@ -281,94 +279,53 @@ public class AlignViewport extends AlignmentViewport implements false); showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false); showConsensus = Cache.getDefault("SHOW_IDENTITY", true); + + showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true); } initAutoAnnotation(); - String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC + String colourProperty = alignment.isNucleotide() + ? Preferences.DEFAULT_COLOUR_NUC : Preferences.DEFAULT_COLOUR_PROT; - String propertyValue = Cache.getProperty(colourProperty); - if (propertyValue == null) - { - // fall back on this property for backwards compatibility - propertyValue = Cache.getProperty(Preferences.DEFAULT_COLOUR); - } - if (propertyValue != null) + String schemeName = Cache.getProperty(colourProperty); + if (schemeName == null) { - ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme( - alignment, propertyValue); - globalColourScheme = new CollectionColourScheme(colourScheme); - - if (colourScheme instanceof UserColourScheme) - { - globalColourScheme = new CollectionColourScheme( - UserDefinedColours.loadDefaultColours()); - globalColourScheme.setThreshold(0, isIgnoreGapsConsensus()); - } - - if (globalColourScheme != null) - { - globalColourScheme.setConsensus(hconsensus); - } + // only DEFAULT_COLOUR available in Jalview before 2.9 + schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR, + ResidueColourScheme.NONE); } - } + ColourSchemeI colourScheme = ColourSchemeProperty + .getColourScheme(alignment, schemeName); + residueShading = new ResidueShader(colourScheme); - /** - * 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) + if (colourScheme instanceof UserColourScheme) { - return null; + residueShading = new ResidueShader( + UserDefinedColours.loadDefaultColours()); + residueShading.setThreshold(0, isIgnoreGapsConsensus()); } - StringBuffer seqs = new StringBuffer(); - for (int i = 0; i < consensus.annotations.length; i++) + + if (residueShading != 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); - } - } + residueShading.setConsensus(hconsensus); } - - SequenceI sq = new Sequence("Consensus", seqs.toString()); - sq.setDescription("Percentage Identity Consensus " - + ((ignoreGapsInConsensusCalculation) ? " without gaps" : "")); - return sq; } boolean validCharWidth; /** - * update view settings with the given font. You may need to call - * alignPanel.fontChanged to update the layout geometry - * - * @param setGrid - * when true, charWidth/height is set according to font mentrics + * {@inheritDoc} */ + @Override public void setFont(Font f, boolean setGrid) { font = f; Container c = new Container(); - java.awt.FontMetrics fm = c.getFontMetrics(font); - int w = viewStyle.getCharWidth(), ww = fm.charWidth('M'), h = viewStyle - .getCharHeight(); if (setGrid) { + FontMetrics fm = c.getFontMetrics(font); + int ww = fm.charWidth('M'); setCharHeight(fm.getHeight()); setCharWidth(ww); } @@ -385,7 +342,6 @@ public class AlignViewport extends AlignmentViewport implements super.setViewStyle(settingsForView); setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(), viewStyle.getFontSize()), false); - } /** @@ -491,27 +447,6 @@ public class AlignViewport extends AlignmentViewport implements } /** - * DOCUMENT ME! - * - * @param tree - * DOCUMENT ME! - */ - public void setCurrentTree(NJTree tree) - { - currentTree = tree; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public NJTree getCurrentTree() - { - return currentTree; - } - - /** * returns the visible column regions of the alignment * * @param selectedRegionOnly @@ -519,10 +454,10 @@ public class AlignViewport extends AlignmentViewport implements * area * @return */ - public int[] getViewAsVisibleContigs(boolean selectedRegionOnly) + public Iterator getViewAsVisibleContigs(boolean selectedRegionOnly) { - int[] viscontigs = null; - int start = 0, end = 0; + int start = 0; + int end = 0; if (selectedRegionOnly && selectionGroup != null) { start = selectionGroup.getStartRes(); @@ -532,8 +467,7 @@ public class AlignViewport extends AlignmentViewport implements { end = alignment.getWidth(); } - viscontigs = colSel.getVisibleContigs(start, end); - return viscontigs; + return (alignment.getHiddenColumns().getVisContigsIterator(start, end)); } /** @@ -600,9 +534,11 @@ public class AlignViewport extends AlignmentViewport implements public void sendSelection() { jalview.structure.StructureSelectionManager - .getStructureSelectionManager(Desktop.instance).sendSelection( - new SequenceGroup(getSelectionGroup()), - new ColumnSelection(getColumnSelection()), this); + .getStructureSelectionManager(Desktop.instance) + .sendSelection(new SequenceGroup(getSelectionGroup()), + new ColumnSelection(getColumnSelection()), + new HiddenColumns(getAlignment().getHiddenColumns()), + this); } /** @@ -615,8 +551,8 @@ public class AlignViewport extends AlignmentViewport implements */ public AlignmentPanel getAlignPanel() { - AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this - .getSequenceSetId()); + AlignmentPanel[] aps = PaintRefresher + .getAssociatedPanels(this.getSequenceSetId()); for (int p = 0; aps != null && p < aps.length; p++) { if (aps[p].av == this) @@ -655,10 +591,10 @@ public class AlignViewport extends AlignmentViewport implements */ public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries) { - List seqvectors = new ArrayList(); + List seqvectors = new ArrayList<>(); for (PDBEntry pdb : pdbEntries) { - List choosenSeqs = new ArrayList(); + List choosenSeqs = new ArrayList<>(); for (SequenceI sq : alignment.getSequences()) { Vector pdbRefEntries = sq.getDatasetSequence() @@ -675,8 +611,7 @@ public class AlignViewport extends AlignmentViewport implements && pdb.getChainCode() != null) { if (pdbRefEntry.getChainCode().equalsIgnoreCase( - pdb.getChainCode()) - && !choosenSeqs.contains(sq)) + pdb.getChainCode()) && !choosenSeqs.contains(sq)) { choosenSeqs.add(sq); continue; @@ -721,7 +656,7 @@ public class AlignViewport extends AlignmentViewport implements return validCharWidth; } - private Hashtable calcIdParams = new Hashtable(); + private Hashtable calcIdParams = new Hashtable<>(); public AutoCalcSetting getCalcIdSettingsFor(String calcId) { @@ -751,7 +686,8 @@ public class AlignViewport extends AlignmentViewport implements *
    *
  • compute the equivalent edit on the mapped sequences
    • *
  • apply the mapped edit
    • - *
  • 'apply' the source edit to the working copy of the source sequences
    • + *
  • 'apply' the source edit to the working copy of the source + * sequences
    • *
* * @param command @@ -857,7 +793,7 @@ public class AlignViewport extends AlignmentViewport implements } } - setEndSeq(getAlignment().getHeight()); + ranges.setEndSeq(getAlignment().getHeight()); firePropertyChange("alignment", null, getAlignment().getSequences()); } @@ -872,8 +808,7 @@ public class AlignViewport extends AlignmentViewport implements */ protected boolean openLinkedAlignment(AlignmentI al, String title) { - String[] options = new String[] { - MessageManager.getString("action.no"), + String[] options = new String[] { MessageManager.getString("action.no"), MessageManager.getString("label.split_window"), MessageManager.getString("label.new_window"), }; final String question = JvSwingUtils.wrapTooltip(true, @@ -915,8 +850,9 @@ public class AlignViewport extends AlignmentViewport implements AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); newAlignFrame.setTitle(title); - newAlignFrame.statusBar.setText(MessageManager.formatMessage( - "label.successfully_loaded_file", new Object[] { title })); + newAlignFrame.statusBar.setText(MessageManager + .formatMessage("label.successfully_loaded_file", new Object[] + { title })); // TODO if we want this (e.g. to enable reload of the alignment from file), // we will need to add parameters to the stack. @@ -933,8 +869,8 @@ public class AlignViewport extends AlignmentViewport implements try { - newAlignFrame.setMaximum(jalview.bin.Cache.getDefault( - "SHOW_FULLSCREEN", false)); + newAlignFrame.setMaximum( + jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false)); } catch (java.beans.PropertyVetoException ex) { } @@ -966,8 +902,8 @@ public class AlignViewport extends AlignmentViewport implements * is protein, the mappings to cDNA will be registered with * StructureSelectionManager as a side-effect. */ - AlignFrame copyMe = new AlignFrame(complement, - AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + AlignFrame copyMe = new AlignFrame(complement, AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); copyMe.setTitle(getAlignPanel().alignFrame.getTitle()); AlignmentI al = newAlignFrame.viewport.getAlignment(); @@ -1052,8 +988,9 @@ public class AlignViewport extends AlignmentViewport implements // TODO would like next line without cast but needs more refactoring... final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement()) .getAlignPanel(); - complementPanel.setDontScrollComplement(true); + complementPanel.setToScrollComplementPanel(false); complementPanel.scrollToCentre(sr, verticalOffset); + complementPanel.setToScrollComplementPanel(true); } } @@ -1150,5 +1087,4 @@ public class AlignViewport extends AlignmentViewport implements } fr.setTransparency(featureSettings.getTransparency()); } - }