X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=835371f1c6ed45585088e9b073d3201adaf5172c;hb=ac556c533791c50fd03029357eedce928991213b;hp=e0efa7ca91bc285e1ade8cefe8f3a17ceb141a0f;hpb=c00cfcb9f2223f1225fba57e5de85141cfa4570c;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index e0efa7c..835371f 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; @@ -35,10 +35,10 @@ 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.renderer.ResidueShader; @@ -46,7 +46,6 @@ 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; @@ -57,6 +56,7 @@ 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; @@ -72,11 +72,11 @@ import javax.swing.JInternalFrame; * @version $Revision: 1.141 $ */ public class AlignViewport extends AlignmentViewport implements - SelectionSource, CommandListener + SelectionSource { Font font; - NJTree currentTree = null; + TreeModel currentTree = null; boolean cursorMode = false; @@ -105,7 +105,7 @@ public class AlignViewport extends AlignmentViewport implements */ public AlignViewport(AlignmentI al) { - setAlignment(al); + super(al); init(); } @@ -123,6 +123,7 @@ 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 @@ -135,8 +136,8 @@ public class AlignViewport extends AlignmentViewport implements { Cache.log.debug("Setting viewport's view id : " + viewId); } - setAlignment(al); init(); + } /** @@ -147,12 +148,12 @@ 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(); } @@ -165,7 +166,7 @@ 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); @@ -181,9 +182,10 @@ 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 @@ -196,10 +198,10 @@ public class AlignViewport extends AlignmentViewport implements { Cache.log.debug("Setting viewport's view id : " + viewId); } - setAlignment(al); + if (hiddenColumns != null) { - colSel = hiddenColumns; + al.setHiddenColumns(hiddenColumns); } init(); } @@ -238,10 +240,6 @@ public class AlignViewport extends AlignmentViewport implements 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"); @@ -282,6 +280,8 @@ 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 @@ -310,64 +310,22 @@ public class AlignViewport extends AlignmentViewport implements } } - /** - * 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; - } - 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); } @@ -494,7 +452,7 @@ public class AlignViewport extends AlignmentViewport implements * @param tree * DOCUMENT ME! */ - public void setCurrentTree(NJTree tree) + public void setCurrentTree(TreeModel tree) { currentTree = tree; } @@ -504,7 +462,7 @@ public class AlignViewport extends AlignmentViewport implements * * @return DOCUMENT ME! */ - public NJTree getCurrentTree() + public TreeModel getCurrentTree() { return currentTree; } @@ -530,7 +488,7 @@ public class AlignViewport extends AlignmentViewport implements { end = alignment.getWidth(); } - viscontigs = colSel.getVisibleContigs(start, end); + viscontigs = alignment.getHiddenColumns().getVisibleContigs(start, end); return viscontigs; } @@ -600,7 +558,9 @@ public class AlignViewport extends AlignmentViewport implements jalview.structure.StructureSelectionManager .getStructureSelectionManager(Desktop.instance).sendSelection( new SequenceGroup(getSelectionGroup()), - new ColumnSelection(getColumnSelection()), this); + new ColumnSelection(getColumnSelection()), + new HiddenColumns(getAlignment().getHiddenColumns()), + this); } /** @@ -855,7 +815,7 @@ public class AlignViewport extends AlignmentViewport implements } } - setEndSeq(getAlignment().getHeight()); + ranges.setEndSeq(getAlignment().getHeight()); firePropertyChange("alignment", null, getAlignment().getSequences()); } @@ -1050,8 +1010,9 @@ 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); } }