"JALVIEW_ANNOTATION\n"\r
+ "# Created: "\r
+ new java.util.Date() + "\n\n");\r
-\r
+ /**\r
+ * convenience method for pre-2.4 feature files which have no view, hidden columns or hidden row keywords.\r
+ * @param annotations\r
+ * @param groups\r
+ * @param properties\r
+ * @return feature file as a string.\r
+ */\r
public String printAnnotations(AlignmentAnnotation[] annotations,\r
Vector groups,\r
Hashtable properties)\r
{\r
+ return printAnnotations(annotations, groups,\r
+ properties, null);\r
+\r
+ }\r
+ /**\r
+ * hold all the information about a particular view definition\r
+ * read from or written out in an annotations file.\r
+ */\r
+ public class ViewDef {\r
+ public String viewname;\r
+ public HiddenSequences hidseqs;\r
+ public ColumnSelection hiddencols;\r
+ public Vector visibleGroups;\r
+ public ViewDef(String viewname, HiddenSequences hidseqs,\r
+ ColumnSelection hiddencols)\r
+ {\r
+ this.viewname = viewname;\r
+ this.hidseqs = hidseqs;\r
+ this.hiddencols = hiddencols;\r
+ }\r
+ }\r
+ public String printAnnotations(AlignmentAnnotation[] annotations,\r
+ Vector groups,\r
+ Hashtable properties, ViewDef[] views)\r
+ {\r
if (annotations != null)\r
{\r
boolean oneColour = true;\r
{\r
row = annotations[i];\r
\r
- if (!row.visible)\r
+ if (!row.visible && !row.hasScore())\r
{\r
continue;\r
}\r
text.append(row.description + "\t");\r
}\r
\r
- for (int j = 0; j < row.annotations.length; j++)\r
+ for (int j = 0; row.annotations!=null && j < row.annotations.length; j++)\r
{\r
if (refSeq != null &&\r
jalview.util.Comparison.isGap(refSeq.getCharAt(j)))\r
}\r
\r
color = row.annotations[j].colour;\r
- if (row.annotations[j].value != 0f)\r
+ if (row.annotations[j].value != 0f && row.annotations[j].value!=Float.NaN) \r
{\r
text.append(comma + row.annotations[j].value);\r
}\r
}\r
\r
}\r
-\r
+ \r
return text.toString();\r
}\r
\r
{\r
text.append("textColThreshold=" + sg.thresholdTextColour);\r
}\r
+ if (sg.idColour!=null)\r
+ {\r
+ text.append("idColour="+jalview.util.Format.getHexString(sg.idColour)+"\t");\r
+ }\r
\r
text.append("\n\n");\r
\r
}\r
\r
SequenceI refSeq = null;\r
+ String refSeqId = null;\r
public boolean readAnnotationFile(AlignmentI al,\r
String file,\r
String protocol)\r
\r
else if (token.equalsIgnoreCase("SEQUENCE_REF"))\r
{\r
- refSeq = al.findName(st.nextToken());\r
+ if (st.hasMoreTokens())\r
+ {\r
+ refSeq = al.findName(refSeqId=st.nextToken());\r
+ if (refSeq==null)\r
+ {\r
+ refSeqId=null;\r
+ }\r
try\r
{\r
refSeqIndex = Integer.parseInt(st.nextToken());\r
{\r
refSeqIndex = 1;\r
}\r
-\r
+ } else {\r
+ refSeq = null;\r
+ refSeqId = null;\r
+ }\r
continue ;\r
}\r
\r
\r
annotation = new AlignmentAnnotation(label,\r
description,\r
- annotations,\r
+ (index==0) ? null : annotations,\r
0,\r
0,\r
graphStyle);\r
if (refSeq != null)\r
{\r
annotation.belowAlignment=false;\r
- annotation.createSequenceMapping(refSeq, refSeqIndex, false);\r
- annotation.adjustForAlignment();\r
- refSeq.addAlignmentAnnotation(annotation);\r
- }\r
-\r
- al.addAnnotation(annotation);\r
-\r
- al.setAnnotationIndex(annotation,\r
+ do {\r
+ // copy before we do any mapping business.\r
+ // TODO: verify that undo/redo with 1:many sequence associated annotations can be undone correctly\r
+ AlignmentAnnotation ann = new AlignmentAnnotation(annotation);\r
+ annotation.createSequenceMapping(refSeq, refSeqIndex, false);\r
+ annotation.adjustForAlignment();\r
+ refSeq.addAlignmentAnnotation(annotation);\r
+ al.addAnnotation(annotation);\r
+ al.setAnnotationIndex(annotation,\r
+ al.getAlignmentAnnotation().length - existingAnnotations -\r
+ 1);\r
+ // and recover our virgin copy to use again if necessary.\r
+ annotation = ann;\r
+ \r
+ } while (refSeqId!=null && (refSeq=al.findName(refSeq, refSeqId, true))!=null);\r
+ } else {\r
+ al.addAnnotation(annotation);\r
+ al.setAnnotationIndex(annotation,\r
al.getAlignmentAnnotation().length - existingAnnotations -\r
1);\r
+ }\r
}\r
\r
}\r
displayChar = desc;\r
desc = tmp;\r
}\r
-\r
+ /*\r
+ * In principle, this code will ensure that the Annotation element generated is renderable by any of the applet or application rendering code\r
+ * but instead we check for null strings when the display character is rendered. \r
+ if (displayChar==null)\r
+ {\r
+ displayChar="";\r
+ }\r
+ */\r
Annotation anot = new Annotation(displayChar, desc, ss, value);\r
\r
anot.colour = colour;\r
if (sg != null)\r
{\r
String keyValue, key, value;\r
+ ColourSchemeI def = sg.cs;\r
+ sg.cs = null;\r
while (st.hasMoreTokens())\r
{\r
keyValue = st.nextToken();\r
{\r
sg.thresholdTextColour = Integer.parseInt(value);\r
}\r
-\r
+ else if (key.equalsIgnoreCase("idColour"))\r
+ {\r
+ // consider warning if colour doesn't resolve to a real colour\r
+ sg.setIdColour((def = new UserColourScheme(value)).findColour('A'));\r
+ }\r
sg.recalcConservation();\r
}\r
+ if (sg.cs==null)\r
+ {\r
+ sg.cs = def;\r
+ }\r
}\r
}\r
\r
al.setProperty(key,value);\r
}\r
}\r
+\r
+ /**\r
+ * Write annotations as a CSV file of the form 'label, value, value, ...' for each row.\r
+ * @param annotations\r
+ * @return CSV file as a string.\r
+ */\r
+ public String printCSVAnnotations(AlignmentAnnotation[] annotations)\r
+ {\r
+ StringBuffer sp = new StringBuffer();\r
+ for (int i=0; i<annotations.length; i++)\r
+ {\r
+ String atos = annotations[i].toString();\r
+ int p = 0;\r
+ do {\r
+ int cp = atos.indexOf("\n", p);\r
+ sp.append(annotations[i].label);\r
+ sp.append(",");\r
+ if (cp>p)\r
+ {\r
+ sp.append(atos.substring(p, cp+1));\r
+ } else {\r
+ sp.append(atos.substring(p));\r
+ sp.append("\n");\r
+ }\r
+ p = cp+1;\r
+ } while (p>0);\r
+ }\r
+ return sp.toString();\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff