return jalview.bin.Cache.getProperty("VERSION");\r
}\r
\r
+ public FeatureRenderer getFeatureRenderer()\r
+ {\r
+ return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();\r
+ }\r
+\r
\r
public void fetchSequence_actionPerformed(ActionEvent e)\r
{\r
String newtitle = new String("Copied sequences");\r
\r
//>>>This is a fix for the moment, until a better solution is found!!<<<\r
- FeatureRenderer fr = af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer();\r
- fr.featureColours = alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours;\r
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(\r
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer());\r
+\r
\r
if (title.startsWith("Copied sequences"))\r
{\r
\r
//Jalview no longer allows deletion of residues.\r
//Check here whether any residues are in selection area\r
- if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)\r
+ /* if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)\r
{\r
for (int i = 0; i < sg.sequences.size(); i++)\r
{\r
j++;\r
}while(j<=sg.getEndRes());\r
}\r
- }\r
+ }*/\r
\r
\r
addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
\r
viewport.padGaps = padGapsMenuitem.isSelected();\r
\r
- if (viewport.padGaps)\r
- alignmentChanged();\r
+ // if (viewport.padGaps)\r
+ alignmentChanged();\r
}\r
\r
/**\r
{\r
// Add any Multiple Sequence Alignment Services\r
final JMenu msawsmenu = new JMenu("Alignment");\r
+ final AlignFrame af = this;\r
for (int i = 0, j = msaws.size(); i < j; i++)\r
{\r
final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.\r
{\r
SequenceI[] msa = gatherSequencesForAlignment();\r
new jalview.ws.MsaWSClient(sh, title, msa,\r
- false, true, viewport.getAlignment().getDataset());\r
+ false, true, viewport.getAlignment().getDataset(), af);\r
\r
}\r
\r
{\r
SequenceI[] msa = gatherSequencesForAlignment();\r
new jalview.ws.MsaWSClient(sh, title, msa,\r
- true, true, viewport.getAlignment().getDataset());\r
+ true, true, viewport.getAlignment().getDataset(), af);\r
\r
}\r
\r
}\r
\r
// This method will attempt to load a "dropped" file first by testing\r
- // whether its and Annotation file, then group file. If both are\r
+ // whether its and Annotation file, then features file. If both are\r
// false then the user may have dropped an alignment file onto this\r
// AlignFrame\r
- void loadJalviewDataFile(String file)\r
+ public void loadJalviewDataFile(String file)\r
{\r
try{\r
boolean isAnnotation = new AnnotationReader().readAnnotationFile(viewport.\r