X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=c22a37dca5ee02a31678e681488f9508ac9fa23f;hb=7544cc610aa35fd10e975598cc8fb2c97abe6bd9;hp=288f261eb3f13f161cf7b1f152b7c4d1294faec4;hpb=2d3be0b3f26fa3e35480976cd5a90a5562d43dcf;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 288f261..c22a37d 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -34,13 +34,11 @@ import jalview.commands.CommandI; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; -import jalview.datamodel.Annotation; 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; @@ -73,8 +71,8 @@ import javax.swing.JInternalFrame; * @author $author$ * @version $Revision: 1.141 $ */ -public class AlignViewport extends AlignmentViewport implements - SelectionSource +public class AlignViewport extends AlignmentViewport + implements SelectionSource { Font font; @@ -131,8 +129,8 @@ public class AlignViewport extends AlignmentViewport implements // 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) { @@ -193,8 +191,8 @@ public class AlignViewport extends AlignmentViewport implements // 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) { @@ -227,17 +225,17 @@ 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() @@ -286,7 +284,8 @@ public class AlignViewport extends AlignmentViewport implements 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 schemeName = Cache.getProperty(colourProperty); if (schemeName == null) @@ -295,8 +294,8 @@ public class AlignViewport extends AlignmentViewport implements schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR, ResidueColourScheme.NONE); } - ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme( - alignment, schemeName); + ColourSchemeI colourScheme = ColourSchemeProperty + .getColourScheme(alignment, schemeName); residueShading = new ResidueShader(colourScheme); if (colourScheme instanceof UserColourScheme) @@ -312,47 +311,6 @@ 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++) - { - Annotation annotation = consensus.annotations[i]; - if (annotation != null) - { - String description = annotation.description; - if (description != null && description.startsWith("[")) - { - // consensus is a tie - just pick the first one - seqs.append(description.charAt(1)); - } - else - { - seqs.append(annotation.displayCharacter); - } - } - } - - SequenceI sq = new Sequence("Consensus", seqs.toString()); - sq.setDescription("Percentage Identity Consensus " - + ((ignoreGapsInConsensusCalculation) ? " without gaps" : "")); - return sq; - } - boolean validCharWidth; /** @@ -599,8 +557,8 @@ public class AlignViewport extends AlignmentViewport implements public void sendSelection() { jalview.structure.StructureSelectionManager - .getStructureSelectionManager(Desktop.instance).sendSelection( - new SequenceGroup(getSelectionGroup()), + .getStructureSelectionManager(Desktop.instance) + .sendSelection(new SequenceGroup(getSelectionGroup()), new ColumnSelection(getColumnSelection()), new HiddenColumns(getAlignment().getHiddenColumns()), this); @@ -616,8 +574,8 @@ 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) @@ -676,8 +634,7 @@ 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; @@ -752,7 +709,8 @@ public class AlignViewport extends AlignmentViewport implements * * * @param command @@ -873,8 +831,7 @@ 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, @@ -916,8 +873,9 @@ 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. @@ -934,8 +892,8 @@ 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) { } @@ -967,8 +925,8 @@ 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();