X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcontroller%2FAlignViewController.java;h=9b8a9e3d868149de96b461c28ef4b07bd9dbf9eb;hb=ccf06ac048c367e28d5e41a569bd95d5a2a77989;hp=a5a35910c1b5d9ac7139d4c228d2cb5354a87835;hpb=6c2b68627777b6731f3e1081fb7437b9678c9670;p=jalview.git diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java index a5a3591..9b8a9e3 100644 --- a/src/jalview/controller/AlignViewController.java +++ b/src/jalview/controller/AlignViewController.java @@ -107,8 +107,7 @@ public class AlignViewController implements AlignViewControllerI viewport.getAlignment().addGroup(gps[g]); if (colours != null) { - gps[g].setColourScheme(colours.getInstance(viewport, gps[g], - viewport.getHiddenRepSequences())); + gps[g].setColourScheme(colours.getInstance(viewport, gps[g])); } Color col = new Color((int) (Math.random() * 255), (int) (Math.random() * 255), (int) (Math.random() * 255)); @@ -167,9 +166,10 @@ public class AlignViewController implements AlignViewControllerI // 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(); - SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null - || extendCurrent) ? viewport.getAlignment() - : viewport.getSelectionGroup(); + boolean searchSelection = viewport.getSelectionGroup() != null + && !extendCurrent; + SequenceCollectionI sqcol = searchSelection ? viewport + .getSelectionGroup() : viewport.getAlignment(); int nseq = findColumnsWithFeature(featureType, sqcol, bs); @@ -205,9 +205,10 @@ public class AlignViewController implements AlignViewControllerI } else { - avcg.setStatus(MessageManager - .formatMessage("label.no_feature_of_type_found", new String[] - { featureType })); + String key = searchSelection ? "label.no_feature_found_selection" + : "label.no_feature_of_type_found"; + avcg.setStatus(MessageManager.formatMessage(key, + new String[] { featureType })); if (!extendCurrent) { cs.clear(); @@ -354,7 +355,7 @@ public class AlignViewController implements AlignViewControllerI } @Override - public boolean parseFeaturesFile(String file, DataSourceType protocol, + public boolean parseFeaturesFile(Object file, DataSourceType protocol, boolean relaxedIdMatching) { boolean featuresAdded = false;