import jalview.datamodel.*;\r
import java.util.StringTokenizer;\r
import jalview.schemes.UserColourScheme;\r
-import jalview.gui.FeatureRenderer;\r
+import java.net.URL;\r
\r
public class AnnotationReader\r
{\r
- public boolean readGroupsFile(FeatureRenderer fr, AlignmentI al, String file)\r
+ public boolean readAnnotationFile(AlignmentI al, String file)\r
{\r
+\r
try\r
{\r
- BufferedReader in = new BufferedReader(new FileReader(file));\r
- SequenceI seq = null;\r
- String line, type, desc, token;\r
-\r
- int index, start, end;\r
- StringTokenizer st;\r
- SequenceFeature sf;\r
- int lineNo = 0;\r
- while ( (line = in.readLine()) != null)\r
+ BufferedReader in = null;\r
+ java.io.InputStream is = getClass().getResourceAsStream("/" + file);\r
+ if (is != null)\r
{\r
- lineNo++;\r
- st = new StringTokenizer(line, "\t");\r
- if (st.countTokens() == 2)\r
+ in = new BufferedReader(new java.io.InputStreamReader(is));\r
+ }\r
+ else\r
+ {\r
+ try\r
{\r
- type = st.nextToken();\r
- UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
- fr.setColour(type, ucs.findColour("A"));\r
- continue;\r
+ URL url = new URL(file);\r
+ in = new BufferedReader(new InputStreamReader(url.openStream()));\r
}\r
-\r
- while (st.hasMoreElements())\r
+ catch (java.net.MalformedURLException ex)\r
{\r
- desc = st.nextToken();\r
- token = st.nextToken();\r
- if (!token.equals("ID_NOT_SPECIFIED"))\r
- {\r
- index = al.findIndex(al.findName(token));\r
- st.nextToken();\r
- }\r
- else\r
- {\r
- index = Integer.parseInt(st.nextToken());\r
- }\r
-\r
- start = Integer.parseInt(st.nextToken());\r
- end = Integer.parseInt(st.nextToken());\r
-\r
- seq = al.getSequenceAt(index);\r
- start = seq.findIndex(start) - 1;\r
- end = seq.findIndex(end) - 1;\r
-\r
- type = st.nextToken();\r
-\r
- if (fr.getColour(type) == null)\r
- {\r
- // Probably the old style groups file\r
- UserColourScheme ucs = new UserColourScheme(type);\r
- fr.setColour(type, ucs.findColour("A"));\r
- }\r
-\r
- sf = new SequenceFeature(type, desc, "", start, end);\r
-\r
- seq.getDatasetSequence().addSequenceFeature(sf);\r
+ in = new BufferedReader(new FileReader(file));\r
}\r
}\r
- }\r
- catch (Exception ex)\r
- {\r
- System.out.println("Error parsing groups file: " + ex);\r
- return false;\r
- }\r
-\r
- return true;\r
- }\r
\r
- public boolean readAnnotationFile(AlignmentI al, String file)\r
- {\r
- try\r
- {\r
- BufferedReader in = new BufferedReader(new FileReader(file));\r
String line, label, description, token;\r
int graphStyle, index;\r
SequenceI refSeq = null;\r
- int refSeqIndex = -1;\r
+ int refSeqIndex = 1;\r
+ int existingAnnotations = 0;\r
+ if(al.getAlignmentAnnotation()!=null)\r
+ existingAnnotations = al.getAlignmentAnnotation().length;\r
\r
+ int alWidth = al.getWidth();\r
\r
StringTokenizer st;\r
Annotation[] annotations;\r
try{\r
refSeqIndex = Integer.parseInt(st.nextToken());\r
}\r
- catch(NumberFormatException ex)\r
+ catch(Exception ex)\r
{\r
- refSeqIndex = 0;\r
+ refSeqIndex = 1;\r
}\r
\r
continue;\r
}\r
\r
+\r
graphStyle = AlignmentAnnotation.getGraphValueFromString(token);\r
label = description = st.nextToken();\r
\r
line = st.nextToken();\r
+\r
st = new StringTokenizer(line, "|", true);\r
- annotations = new Annotation[st.countTokens()];\r
+ annotations = new Annotation[alWidth];\r
+\r
index = 0;\r
boolean emptyColumn = true;\r
- while (st.hasMoreElements())\r
+\r
+\r
+ while (st.hasMoreElements() && index<alWidth)\r
{\r
token = st.nextToken().trim();\r
-\r
if(token.equals("|"))\r
{\r
if(emptyColumn)\r
- annotations[index++] = parseAnnotation("");\r
+ index++;\r
\r
emptyColumn = true;\r
}\r
0,\r
graphStyle);\r
\r
- al.addAnnotation(annotation, refSeq, refSeqIndex);\r
+ if(refSeq!=null)\r
+ {\r
+ annotation.createSequenceMapping(refSeq, refSeqIndex);\r
+ refSeq.addAlignmentAnnotation(annotation);\r
+ }\r
\r
+ al.addAnnotation(annotation);\r
+\r
+ al.setAnnotationIndex(annotation, al.getAlignmentAnnotation().length - existingAnnotations-1);\r
}\r
+\r
}catch(Exception ex)\r
- {ex.printStackTrace();\r
- // System.out.println("Problem reading annotation file: "+ex);\r
+ {\r
+ ex.printStackTrace();\r
+ System.out.println("Problem reading annotation file: "+ex);\r
return false;\r
}\r
return true;\r
String desc = "", displayChar="";\r
char ss = ' '; // secondaryStructure\r
float value = 0;\r
+ boolean parsedValue = false;\r
StringTokenizer st = new StringTokenizer(string, ",");\r
String token;\r
while(st.hasMoreTokens())\r
if(token.length()==0)\r
continue;\r
\r
- if(value==0)\r
- { try{\r
- value = Float.parseFloat(token);\r
+ if(!parsedValue)\r
+ {\r
+ try{\r
+ value = new Float(token).floatValue();\r
+ displayChar = token;\r
+ parsedValue = true;\r
}catch(NumberFormatException ex){}\r
}\r
\r
- if(token.length()==1)\r
+ if(token.equals("H") || token.equals("E"))\r
{\r
// Either this character represents a helix or sheet\r
// or an integer which can be displayed\r
- if(token.equals("H") || token.equals("E"))\r
- {\r
- ss = token.charAt(0);\r
- }\r
- else //if(value!=0)\r
- {\r
- displayChar = token;\r
- }\r
+ ss = token.charAt(0);\r
}\r
else if(desc.length()<1)\r
desc = token;\r
- else\r
- displayChar = token;\r
+\r
}\r
\r
return new Annotation(displayChar, desc, ss, value);\r
\r
if(annotation==null)\r
return;\r
-\r
- float value = Float.parseFloat(st.nextToken());\r
+ float value = new Float(st.nextToken()).floatValue();\r
String label = st.hasMoreTokens() ? st.nextToken() : null;\r
java.awt.Color colour = null;\r
if(st.hasMoreTokens())\r
colour = ucs.findColour("A");\r
}\r
\r
- annotation.addGraphLine(new GraphLine(value, label, colour));\r
+ annotation.setThreshold(new GraphLine(value, label, colour));\r
\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff