+ /////////////////////////////////\r
+ // LOAD VIEWPORT\r
+ Viewport[] views = jms.getViewport();\r
+ Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER\r
+\r
+\r
+ AlignFrame af = new AlignFrame(al);\r
+\r
+ if(hiddenSeqs!=null)\r
+ {\r
+ for(int s=0; s<JSEQ.length; s++)\r
+ {\r
+ for(int r=0; r<JSEQ[s].getHiddenSequencesCount(); r++)\r
+ {\r
+ al.getSequenceAt(s).addHiddenSequence(\r
+ al.getSequenceAt( JSEQ[s].getHiddenSequences(r) )\r
+ );\r
+ }\r
+ }\r
+\r
+ for(int s=0; s<hiddenSeqs.size(); s++)\r
+ {\r
+ af.viewport.hideSequence(\r
+ (jalview.datamodel.SequenceI)hiddenSeqs.elementAt(s));\r
+ }\r
+ }\r
+\r
+\r
+ if(hideConsensus || hideQuality || hideConservation)\r
+ {\r
+ int hSize = al.getAlignmentAnnotation().length;\r
+ for (int h = 0; h < hSize; h++)\r
+ {\r
+ if (\r
+ (hideConsensus &&\r
+ al.getAlignmentAnnotation()[h].label.equals("Consensus"))\r
+ ||\r
+ (hideQuality &&\r
+ al.getAlignmentAnnotation()[h].label.equals("Quality"))\r
+ ||\r
+ (hideConservation &&\r
+ al.getAlignmentAnnotation()[h].label.equals("Conservation")))\r
+ {\r
+ al.deleteAnnotation(al.getAlignmentAnnotation()[h]);\r
+ hSize--;\r
+ h--;\r
+ }\r
+ }\r
+ af.alignPanel.adjustAnnotationHeight();\r
+ }\r