X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcontroller%2FAlignViewController.java;h=972b6ab43282f0ef9e913b452a146ba3ddbfbcae;hb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;hp=74161c8d1fb3f33b3e8a2ccba37eb4a2c0de7f94;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java index 74161c8..972b6ab 100644 --- a/src/jalview/controller/AlignViewController.java +++ b/src/jalview/controller/AlignViewController.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,62 +20,85 @@ */ package jalview.controller; -import java.awt.Color; -import java.util.BitSet; -import java.util.List; - +import jalview.analysis.AlignmentSorter; import jalview.api.AlignViewControllerGuiI; import jalview.api.AlignViewControllerI; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; +import jalview.api.FeatureRenderer; +import jalview.commands.OrderCommand; import jalview.datamodel.AlignmentI; -import jalview.datamodel.AnnotatedCollectionI; import jalview.datamodel.ColumnSelection; import jalview.datamodel.SequenceCollectionI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.util.MessageManager; + +import java.awt.Color; +import java.util.ArrayList; +import java.util.BitSet; +import java.util.List; public class AlignViewController implements AlignViewControllerI { - AlignViewportI viewport=null; - AlignmentViewPanel alignPanel=null; + AlignViewportI viewport = null; + + AlignmentViewPanel alignPanel = null; + /** * the GUI container that is handling interactions with the user */ private AlignViewControllerGuiI avcg; + @Override - protected void finalize() throws Throwable { + protected void finalize() throws Throwable + { viewport = null; alignPanel = null; avcg = null; }; - - public AlignViewController(AlignViewControllerGuiI alignFrame, AlignViewportI viewport, - AlignmentViewPanel alignPanel) + + public AlignViewController(AlignViewControllerGuiI alignFrame, + AlignViewportI viewport, AlignmentViewPanel alignPanel) { this.avcg = alignFrame; - this.viewport=viewport; + this.viewport = viewport; this.alignPanel = alignPanel; } + @Override - public void setViewportAndAlignmentPanel(AlignViewportI viewport,AlignmentViewPanel alignPanel) + public void setViewportAndAlignmentPanel(AlignViewportI viewport, + AlignmentViewPanel alignPanel) { this.alignPanel = alignPanel; this.viewport = viewport; - + } + @Override public boolean makeGroupsFromSelection() { - - if (viewport.getSelectionGroup() != null) + SequenceGroup sg = viewport.getSelectionGroup(); + ColumnSelection cs = viewport.getColumnSelection(); + SequenceGroup[] gps = null; + if (sg != null + && (cs == null || cs.getSelected() == null || cs.size() == 0)) { - SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom( + gps = jalview.analysis.Grouping.makeGroupsFrom( viewport.getSequenceSelection(), viewport.getAlignmentView(true).getSequenceStrings( viewport.getGapCharacter()), viewport.getAlignment() .getGroups()); + } else { + if (cs!=null) { + gps = jalview.analysis.Grouping.makeGroupsFromCols( + (sg == null) ? viewport.getAlignment().getSequencesArray() + : sg.getSequences().toArray(new SequenceI[0]), cs, + viewport.getAlignment().getGroups()); + } + } + if (gps!=null) { viewport.getAlignment().deleteAllGroups(); viewport.clearSequenceColours(); viewport.setSelectionGroup(null); @@ -89,58 +112,66 @@ public class AlignViewController implements AlignViewControllerI (int) (Math.random() * 255), (int) (Math.random() * 255)); col = col.brighter(); for (SequenceI sq : gps[g].getSequences(null)) + { viewport.setSequenceColour(sq, col); + } } return true; } return false; -} + } + @Override public boolean createGroup() { SequenceGroup sg = viewport.getSelectionGroup(); - if (sg!=null) + if (sg != null) { - viewport.getAlignment().addGroup(sg); - return true; - } + viewport.getAlignment().addGroup(sg); + return true; + } return false; } + @Override public boolean unGroup() { SequenceGroup sg = viewport.getSelectionGroup(); - if (sg!=null) + if (sg != null) { - viewport.getAlignment().deleteGroup(sg); - return true; + viewport.getAlignment().deleteGroup(sg); + return true; } return false; } + @Override public boolean deleteGroups() { - if (viewport.getAlignment().getGroups()!=null && viewport.getAlignment().getGroups().size()>0) + if (viewport.getAlignment().getGroups() != null + && viewport.getAlignment().getGroups().size() > 0) { - viewport.getAlignment().deleteAllGroups(); - viewport.clearSequenceColours(); - viewport.setSelectionGroup(null); - return true; + viewport.getAlignment().deleteAllGroups(); + viewport.clearSequenceColours(); + viewport.setSelectionGroup(null); + return true; } return false; } - + @Override - public boolean markColumnsContainingFeatures(boolean invert, boolean extendCurrent, boolean toggle, String featureType) + public boolean markColumnsContainingFeatures(boolean invert, + boolean extendCurrent, boolean toggle, String featureType) { // JBPNote this routine could also mark rows, not just columns. // need a decent query structure to allow all types of feature searches BitSet bs = new BitSet(); - int alw,alStart; - SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null ? viewport.getAlignment() : viewport.getSelectionGroup()); + int alw, alStart; + SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null ? viewport + .getAlignment() : viewport.getSelectionGroup()); alStart = sqcol.getStartRes(); - alw = sqcol.getEndRes()+1; + alw = sqcol.getEndRes() + 1; List seqs = sqcol.getSequences(); int nseq = 0; for (SequenceI sq : seqs) @@ -148,18 +179,12 @@ public class AlignViewController implements AlignViewControllerI int tfeat = 0; if (sq != null) { - SequenceI dsq = sq.getDatasetSequence(); - while (dsq.getDatasetSequence() != null) - { - dsq = dsq.getDatasetSequence(); - } - ; - SequenceFeature[] sf = dsq.getSequenceFeatures(); + SequenceFeature[] sf = sq.getSequenceFeatures(); if (sf != null) { int ist = sq.findIndex(sq.getStart()); int iend = sq.findIndex(sq.getEnd()); - if (iend < alStart || ist> alw) + if (iend < alStart || ist > alw) { // sequence not in region continue; @@ -177,7 +202,7 @@ public class AlignViewController implements AlignViewControllerI int i = sq.findIndex(sfpos.getBegin()); int j = sq.findIndex(sfpos.getEnd()); - if (jalw) + if (j < alStart || i > alw) { // feature is outside selected region continue; @@ -186,7 +211,8 @@ public class AlignViewController implements AlignViewControllerI { i = alStart; } - if (i< ist) { + if (i < ist) + { i = ist; } if (j > alw) @@ -213,7 +239,9 @@ public class AlignViewController implements AlignViewControllerI if (cs == null) { cs = new ColumnSelection(); - } else { + } + else + { if (!extendCurrent) { cs.clear(); @@ -228,12 +256,13 @@ public class AlignViewController implements AlignViewControllerI if (ibs < 0 || i < ibs) { if (toggle && cs.contains(i)) - { - cs.removeElement(i++); - } else - { - cs.addElement(i++); - } + { + cs.removeElement(i++); + } + else + { + cs.addElement(i++); + } } else { @@ -244,12 +273,14 @@ public class AlignViewController implements AlignViewControllerI } else { - for (int i = bs.nextSetBit(alStart); i >= alStart; i = bs.nextSetBit(i + 1)) + for (int i = bs.nextSetBit(alStart); i >= alStart; i = bs + .nextSetBit(i + 1)) { if (toggle && cs.contains(i)) { cs.removeElement(i); - } else + } + else { cs.addElement(i); } @@ -257,16 +288,18 @@ public class AlignViewController implements AlignViewControllerI } viewport.setColumnSelection(cs); alignPanel.paintAlignment(true); - avcg.setStatus((toggle ? "Toggled ": "Marked ") - + (invert ? (alw-alStart) - bs.cardinality() : bs.cardinality()) - + " columns "+(invert ? "not " : "") + "containing features of type " + featureType - + " across " + nseq + " sequence(s)"); + avcg.setStatus(MessageManager.formatMessage("label.view_controller_toggled_marked", + new String[]{ + (toggle ? MessageManager.getString("label.toggled") : MessageManager.getString("label.marked")), + (invert ? (Integer.valueOf((alw - alStart) - bs.cardinality()).toString()):(Integer.valueOf(bs.cardinality()).toString())), + featureType, Integer.valueOf(nseq).toString() + })); return true; } else { - avcg.setStatus("No features of type " + featureType + " found."); - if (!extendCurrent && cs!=null) + avcg.setStatus(MessageManager.formatMessage("label.no_feature_of_type_found", new String[]{featureType})); + if (!extendCurrent && cs != null) { cs.clear(); alignPanel.paintAlignment(true); @@ -274,4 +307,76 @@ public class AlignViewController implements AlignViewControllerI return false; } } + + + + @Override + public void sortAlignmentByFeatureDensity(String[] typ) + { + sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY); + } + + protected void sortBy(String[] typ, String methodText, final String method) + { + FeatureRenderer fr = alignPanel.getFeatureRenderer(); + if (typ == null) + { + typ = fr==null ? null : fr.getDisplayedFeatureTypes(); + } + String gps[] = null; + gps = fr==null ? null : fr.getDisplayedFeatureGroups(); + if (typ != null) + { + ArrayList types = new ArrayList(); + for (int i = 0; i < typ.length; i++) + { + if (typ[i] != null) + { + types.add(typ[i]); + } + typ = new String[types.size()]; + types.toArray(typ); + } + } + if (gps != null) + { + ArrayList grps = new ArrayList(); + + for (int i = 0; i < gps.length; i++) + { + if (gps[i] != null) + { + grps.add(gps[i]); + } + } + gps = new String[grps.size()]; + grps.toArray(gps); + } + AlignmentI al = viewport.getAlignment(); + + int start, stop; + SequenceGroup sg = viewport.getSelectionGroup(); + if (sg != null) + { + start = sg.getStartRes(); + stop = sg.getEndRes(); + } + else + { + start = 0; + stop = al.getWidth(); + } + SequenceI[] oldOrder = al.getSequencesArray(); + AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method); + avcg.addHistoryItem(new OrderCommand(methodText, oldOrder, viewport + .getAlignment())); + alignPanel.paintAlignment(true); + + } + + @Override + public void sortAlignmentByFeatureScore(String[] typ) + { + sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE); + } }