Must save all the feature settings

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 84e3564..d6a0112 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -253,6 +253,32 @@ public class Jalview2XML
                 features.setDescription(sf[index].getDescription());\r
                 features.setType(sf[index].getType());\r
                 features.setFeatureGroup(sf[index].getFeatureGroup());\r
+                features.setScore(sf[index].getScore());\r
+                if(sf[index].links!=null)\r
+                {\r
+                  for(int l=0; l<sf[index].links.size(); l++)\r
+                  {\r
+                    OtherData keyValue = new OtherData();\r
+                    keyValue.setKey("LINK_"+l);\r
+                    keyValue.setValue(sf[index].links.elementAt(l).toString());\r
+                    features.addOtherData(keyValue);\r
+                  }\r
+                }\r
+                if(sf[index].otherDetails!=null)\r
+                {\r
+                  String key;\r
+                  Enumeration keys = sf[index].otherDetails.keys();\r
+                  while(keys.hasMoreElements())\r
+                  {\r
+                    key = keys.nextElement().toString();\r
+                    OtherData keyValue = new OtherData();\r
+                    keyValue.setKey( key );\r
+                    keyValue.setValue(\r
+                        sf[index].otherDetails.get(key).toString());\r
+                    features.addOtherData(keyValue);\r
+                  }\r
+                }\r
+\r
                 jseq.addFeatures(features);\r
                 index ++;\r
               }\r
@@ -597,6 +623,8 @@ public class Jalview2XML
 \r
           String [] renderOrder =\r
               af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;\r
+\r
+          Vector settingsAdded = new Vector();\r
           for(int ro=0; ro<renderOrder.length; ro++)\r
           {\r
             Setting setting = new Setting();\r
@@ -610,8 +638,30 @@ public class Jalview2XML
                 );\r
 \r
             fs.addSetting(setting);\r
+            settingsAdded.addElement(renderOrder[ro]);\r
+          }\r
+\r
+          //Make sure we save none displayed feature settings\r
+          Enumeration en =\r
+              af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();\r
+          while(en.hasMoreElements())\r
+          {\r
+            String key = en.nextElement().toString();\r
+            if(settingsAdded.contains(key))\r
+              continue;\r
+\r
+            Setting setting = new Setting();\r
+            setting.setType(key);\r
+            setting.setColour(\r
+                af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()\r
+                );\r
+\r
+            setting.setDisplay(false);\r
 \r
+            fs.addSetting(setting);\r
+            settingsAdded.addElement(key);\r
           }\r
+\r
           jms.setFeatureSettings(fs);\r
 \r
         }\r
@@ -804,6 +854,7 @@ public class Jalview2XML
 \r
     String loadPDBFile(String file, String pdbId)\r
     {\r
+      System.out.println("load file "+file);\r
       try\r
       {\r
         JarInputStream jin = null;\r
@@ -824,14 +875,15 @@ public class Jalview2XML
         }\r
         while (!entry.getName().equals(pdbId));\r
 \r
-        DataInputStream in = new DataInputStream(jin);\r
+        BufferedReader in = new BufferedReader(new InputStreamReader(jin));\r
         File outFile = File.createTempFile("jalview_pdb", ".txt");\r
         outFile.deleteOnExit();\r
-        DataOutputStream out = new DataOutputStream(new FileOutputStream(outFile));\r
-        int data;\r
-        while ( (data = in.read()) != -1)\r
+        PrintWriter out = new PrintWriter(new FileOutputStream(outFile));\r
+        String data;\r
+\r
+        while ( (data = in.readLine()) != null)\r
         {\r
-          out.write(data);\r
+          out.println(data);\r
         }\r
         out.close();\r
         return outFile.getAbsolutePath();\r
@@ -899,6 +951,17 @@ public class Jalview2XML
                   features[f].getBegin(), features[f].getEnd(),\r
                   features[f].getFeatureGroup());\r
 \r
+              sf.setScore(features[f].getScore());\r
+              for(int od=0; od<features[f].getOtherDataCount(); od++)\r
+              {\r
+                OtherData keyValue = features[f].getOtherData(od);\r
+                if(keyValue.getKey().startsWith("LINK"))\r
+                  sf.addLink(keyValue.getValue());\r
+                else\r
+                  sf.setValue(keyValue.getKey(), keyValue.getValue());\r
+\r
+              }\r
+\r
               al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);\r
             }\r
           }\r
@@ -910,14 +973,17 @@ public class Jalview2XML
               jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();\r
               entry.setId(ids[p].getId());\r
               entry.setType(ids[p].getType());\r
-              if(!pdbloaded.containsKey(ids[p].getId()))\r
+              if (ids[p].getFile() != null)\r
               {\r
-                String tmppdb = loadPDBFile(file, ids[p].getId());\r
-                entry.setFile(tmppdb);\r
-                pdbloaded.put(ids[p].getId(), tmppdb);\r
+                if (!pdbloaded.containsKey(ids[p].getFile()))\r
+                {\r
+                  String tmppdb = loadPDBFile(file, ids[p].getId());\r
+                  entry.setFile(tmppdb);\r
+                  pdbloaded.put(ids[p].getId(), tmppdb);\r
+                }\r
+                else\r
+                  entry.setFile(pdbloaded.get(ids[p].getId()).toString());\r
               }\r
-              else\r
-                entry.setFile(pdbloaded.get(ids[p].getId()).toString());\r
 \r
               al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);\r
             }\r
@@ -1159,16 +1225,11 @@ public class Jalview2XML
         af.viewport.setWrapAlignment(view.getWrapAlignment());\r
         af.wrapMenuItem.setSelected(view.getWrapAlignment());\r
 \r
-        if (view.getWrapAlignment())\r
-        {\r
-            af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
-        }\r
-        else\r
-        {\r
-            af.annotationPanelMenuItem.setState(view.getShowAnnotation());\r
-            af.viewport.setShowAnnotation(view.getShowAnnotation());\r
-            af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
-        }\r
+        af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
+\r
+        af.annotationPanelMenuItem.setState(view.getShowAnnotation());\r
+        af.viewport.setShowAnnotation(view.getShowAnnotation());\r
+        af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
 \r
         af.viewport.setShowBoxes(view.getShowBoxes());\r
         af.viewBoxesMenuItem.setSelected(view.getShowBoxes());\r