"JALVIEW_ANNOTATION\n"\r
+ "# Created: "\r
+ new java.util.Date() + "\n\n");\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
+ Vector groups,\r
+ Hashtable properties, ViewDef[] views)\r
{\r
if (annotations != null)\r
{\r
+ boolean oneColour = true;\r
AlignmentAnnotation row;\r
String comma;\r
- SequenceI seqref = null;\r
+ SequenceI refSeq = null;\r
\r
StringBuffer colours = new StringBuffer();\r
StringBuffer graphLine = new StringBuffer();\r
{\r
row = annotations[i];\r
\r
- if (!row.visible)\r
+ if (!row.visible && !row.hasScore())\r
{\r
continue;\r
}\r
\r
color = null;\r
+ oneColour = true;\r
\r
if (row.sequenceRef == null)\r
{\r
- if (seqref != null)\r
+ if (refSeq != null)\r
{\r
text.append("\nSEQUENCE_REF\tALIGNMENT\n");\r
}\r
\r
- seqref = null;\r
+ refSeq = null;\r
}\r
\r
- else if (seqref == null || seqref != row.sequenceRef)\r
+ else if (refSeq == null || refSeq != row.sequenceRef)\r
{\r
- seqref = row.sequenceRef;\r
- text.append("\nSEQUENCE_REF\t" + seqref.getName() + "\n");\r
+ refSeq = row.sequenceRef;\r
+ text.append("\nSEQUENCE_REF\t" + refSeq.getName() + "\n");\r
}\r
\r
if (row.graph == AlignmentAnnotation.NO_GRAPH)\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 (seqref != null &&\r
- jalview.util.Comparison.isGap(seqref.getCharAt(j)))\r
+ if (refSeq != null &&\r
+ jalview.util.Comparison.isGap(refSeq.getCharAt(j)))\r
{\r
continue;\r
}\r
text.append(comma + row.annotations[j].secondaryStructure);\r
comma = ",";\r
}\r
- if (row.annotations[j].displayCharacter.length() > 0\r
+ if (row.annotations[j].displayCharacter!=null\r
+ && row.annotations[j].displayCharacter.length() > 0\r
&& !row.annotations[j].displayCharacter.equals(" "))\r
{\r
text.append(comma + row.annotations[j].displayCharacter);\r
\r
if (row.annotations[j] != null)\r
{\r
+ if(color!=null && !color.equals(row.annotations[j].colour))\r
+ {\r
+ oneColour = false;\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
+ if(row.annotations[j].colour!=null\r
+ && row.annotations[j].colour!=java.awt.Color.black)\r
+ {\r
+ text.append(comma+"["+\r
+ jalview.util.Format.getHexString(\r
+ row.annotations[j].colour)+"]");\r
+ }\r
}\r
text.append("|");\r
}\r
\r
+ if(row.hasScore())\r
+ text.append("\t"+row.score);\r
+\r
text.append("\n");\r
\r
- if (color != null && color != java.awt.Color.black)\r
+ if (color != null && color != java.awt.Color.black && oneColour)\r
{\r
colours.append("COLOUR\t"\r
+ row.label + "\t"\r
printGroups(groups);\r
}\r
\r
+ if(properties!=null)\r
+ {\r
+ text.append("\n\nALIGNMENT");\r
+ Enumeration en = properties.keys();\r
+ while(en.hasMoreElements())\r
+ {\r
+ String key = en.nextElement().toString();\r
+ text.append("\t"+key+"="+properties.get(key));\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
continue;\r
}\r
\r
- graphStyle = AlignmentAnnotation.getGraphValueFromString(token);\r
- label = st.nextToken();\r
-\r
- if (st.countTokens() > 1)\r
+ else if( token.equalsIgnoreCase("BELOW_ALIGNMENT"))\r
{\r
- description = st.nextToken();\r
+ setBelowAlignment(al, st);\r
+ continue;\r
}\r
- else\r
+ else if( token.equalsIgnoreCase("ALIGNMENT"))\r
{\r
- description = null;\r
+ addAlignmentDetails(al, st);\r
+ continue;\r
}\r
\r
- line = st.nextToken();\r
+ graphStyle = AlignmentAnnotation.getGraphValueFromString(token);\r
+ label = st.nextToken();\r
\r
- st = new StringTokenizer(line, "|", true);\r
- annotations = new Annotation[alWidth];\r
\r
index = 0;\r
- boolean emptyColumn = true;\r
+ annotations = new Annotation[alWidth];\r
+ description = null;\r
+ float score = Float.NaN;\r
\r
- while (st.hasMoreElements() && index < alWidth)\r
+ if(st.hasMoreTokens())\r
{\r
- token = st.nextToken().trim();\r
- if (token.equals("|"))\r
+ line = st.nextToken();\r
+\r
+ if (line.indexOf("|") ==-1)\r
{\r
- if (emptyColumn)\r
- {\r
- index++;\r
- }\r
+ description = line;\r
+ if (st.hasMoreTokens())\r
+ line = st.nextToken();\r
+ }\r
\r
- emptyColumn = true;\r
+ if(st.hasMoreTokens())\r
+ {\r
+ //This must be the score\r
+ score = Float.valueOf(st.nextToken()).floatValue();\r
}\r
- else\r
+\r
+ st = new StringTokenizer(line, "|", true);\r
+\r
+\r
+ boolean emptyColumn = true;\r
+ boolean onlyOneElement = (st.countTokens()==1);\r
+\r
+ while (st.hasMoreElements() && index < alWidth)\r
{\r
- annotations[index++] = parseAnnotation(token);\r
- emptyColumn = false;\r
+ token = st.nextToken().trim();\r
+\r
+ if(onlyOneElement)\r
+ {\r
+ try\r
+ {\r
+ score = Float.valueOf(token).floatValue();\r
+ break;\r
+ }\r
+ catch(NumberFormatException ex){}\r
+ }\r
+\r
+ if (token.equals("|"))\r
+ {\r
+ if (emptyColumn)\r
+ {\r
+ index++;\r
+ }\r
+\r
+ emptyColumn = true;\r
+ }\r
+ else\r
+ {\r
+ annotations[index++] = parseAnnotation(token);\r
+ emptyColumn = false;\r
+ }\r
}\r
+\r
}\r
\r
annotation = new AlignmentAnnotation(label,\r
description,\r
- annotations,\r
+ (index==0) ? null : annotations,\r
0,\r
0,\r
graphStyle);\r
\r
+ annotation.score = score;\r
+\r
if (refSeq != null)\r
{\r
- System.out.println(refSeq.getName()+" "+refSeqIndex);\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
+ annotation.belowAlignment=false;\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
\r
Annotation parseAnnotation(String string)\r
{\r
- String desc = null, displayChar = "";\r
+ String desc = null, displayChar = null;\r
char ss = ' '; // secondaryStructure\r
float value = 0;\r
boolean parsedValue = false;\r
+\r
+ //find colour here\r
+ java.awt.Color colour = null;\r
+ int i=string.indexOf("[");\r
+ int j=string.indexOf("]");\r
+ if(i>-1 && j>-1)\r
+ {\r
+ UserColourScheme ucs = new UserColourScheme();\r
+\r
+ colour = ucs.getColourFromString(string.substring(i+1,j));\r
+\r
+ string = string.substring(0,i)+string.substring(j+1);\r
+ }\r
+\r
StringTokenizer st = new StringTokenizer(string, ",");\r
String token;\r
while (st.hasMoreTokens())\r
\r
}\r
\r
- if (desc == null)\r
- {\r
- desc = value + "";\r
- }\r
-\r
- if (displayChar.length() > 1 && desc.length() == 1)\r
+ if (displayChar!=null\r
+ && displayChar.length() > 1\r
+ && desc!=null\r
+ && desc.length() == 1)\r
{\r
String tmp = displayChar;\r
displayChar = desc;\r
desc = tmp;\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
- return new Annotation(displayChar, desc, ss, value);\r
+ anot.colour = colour;\r
+\r
+ return anot;\r
}\r
\r
void colourAnnotations(AlignmentI al, String label, String colour)\r
}\r
}\r
\r
+\r
+\r
if (refSeq != null)\r
{\r
sg.setStartRes(refSeq.findIndex(sg.getStartRes() + 1) - 1);\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
+ void setBelowAlignment(AlignmentI al, StringTokenizer st)\r
+ {\r
+ String token;\r
+ AlignmentAnnotation aa;\r
+ while(st.hasMoreTokens())\r
+ {\r
+ token = st.nextToken();\r
+ for(int i=0; i<al.getAlignmentAnnotation().length; i++)\r
+ {\r
+ aa = al.getAlignmentAnnotation()[i];\r
+ if(aa.sequenceRef==refSeq && aa.label.equals(token))\r
+ {\r
+ aa.belowAlignment = true;\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ void addAlignmentDetails(AlignmentI al, StringTokenizer st)\r
+ {\r
+ String keyValue, key, value;\r
+ while (st.hasMoreTokens())\r
+ {\r
+ keyValue = st.nextToken();\r
+ key = keyValue.substring(0, keyValue.indexOf("="));\r
+ value = keyValue.substring(keyValue.indexOf("=") + 1);\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