this.hiddenRepSeqs = hiddenRepSeqs;\r
}\r
}\r
+\r
/**\r
- * Prepare an annotation file given a set of annotations, groups, alignment properties and views. \r
+ * Prepare an annotation file given a set of annotations, groups, alignment\r
+ * properties and views.\r
+ * \r
* @param annotations\r
* @param groups\r
* @param properties\r
public String printAnnotations(AlignmentAnnotation[] annotations,\r
Vector groups, Hashtable properties, ViewDef[] views)\r
{\r
- // TODO: resolve views issue : annotationFile could contain visible region, or full data + hidden region specifications for a view.\r
+ // TODO: resolve views issue : annotationFile could contain visible region,\r
+ // or full data + hidden region specifications for a view.\r
if (annotations != null)\r
{\r
boolean oneColour = true;\r
AlignmentAnnotation row;\r
String comma;\r
SequenceI refSeq = null;\r
+ SequenceGroup refGroup = null;\r
\r
StringBuffer colours = new StringBuffer();\r
StringBuffer graphLine = new StringBuffer();\r
refSeq = null;\r
}\r
\r
- else if (refSeq == null || refSeq != row.sequenceRef)\r
+ else\r
+ {\r
+ if (refSeq == null || refSeq != row.sequenceRef)\r
+ {\r
+ refSeq = row.sequenceRef;\r
+ text.append("\nSEQUENCE_REF\t" + refSeq.getName() + "\n");\r
+ }\r
+ }\r
+ // mark any group references for the row\r
+ if (row.groupRef == null)\r
+ {\r
+\r
+ if (refGroup != null)\r
+ {\r
+ text.append("\nGROUP_REF\tALIGNMENT\n");\r
+ }\r
+\r
+ refGroup = null;\r
+ }\r
+ else\r
{\r
- refSeq = row.sequenceRef;\r
- text.append("\nSEQUENCE_REF\t" + refSeq.getName() + "\n");\r
+ if (refGroup == null || refGroup != row.groupRef)\r
+ {\r
+ refGroup = row.groupRef;\r
+ text.append("\nGROUP_REF\t" + refGroup.getName() + "\n");\r
+ }\r
}\r
+\r
boolean hasGlyphs = row.hasIcons, hasLabels = row.hasText, hasValues = row.hasScore, hasText = false;\r
// lookahead to check what the annotation row object actually contains.\r
for (int j = 0; row.annotations != null\r
.equals(" "));\r
hasGlyphs |= (row.annotations[j].secondaryStructure != 0 && row.annotations[j].secondaryStructure != ' ');\r
hasValues |= (row.annotations[j].value != Float.NaN); // NaNs can't\r
- // be\r
- // rendered..\r
+ // be\r
+ // rendered..\r
hasText |= (row.annotations[j].description != null && row.annotations[j].description\r
.length() > 0);\r
}\r
if (row.annotations[j] != null)\r
{\r
comma = "";\r
- if (hasGlyphs) // could be also hasGlyphs || ... \r
+ if (hasGlyphs) // could be also hasGlyphs || ...\r
{\r
\r
text.append(comma);\r
colours.append("COLOUR\t" + row.label + "\t"\r
+ jalview.util.Format.getHexString(color) + "\n");\r
}\r
- if (row.scaleColLabel || row.showAllColLabels || row.centreColLabels)\r
+ if (row.scaleColLabel || row.showAllColLabels\r
+ || row.centreColLabels)\r
{\r
- rowprops.append("ROWPROPERTIES\t"+row.label);\r
- rowprops.append("\tscaletofit="+row.scaleColLabel);\r
- rowprops.append("\tshowalllabs="+row.showAllColLabels);\r
- rowprops.append("\tcentrelabs="+row.centreColLabels);\r
+ rowprops.append("ROWPROPERTIES\t" + row.label);\r
+ rowprops.append("\tscaletofit=" + row.scaleColLabel);\r
+ rowprops.append("\tshowalllabs=" + row.showAllColLabels);\r
+ rowprops.append("\tcentrelabs=" + row.centreColLabels);\r
rowprops.append("\n");\r
}\r
}\r
public boolean readAnnotationFile(AlignmentI al, String file,\r
String protocol)\r
{\r
- Hashtable autoAnnots=new Hashtable();\r
+ String groupRef = null;\r
+ Hashtable groupRefRows = new Hashtable();\r
+\r
+ Hashtable autoAnnots = new Hashtable();\r
try\r
{\r
BufferedReader in = null;\r
int graphStyle, index;\r
int refSeqIndex = 1;\r
int existingAnnotations = 0;\r
- // when true - will add new rows regardless of whether they are duplicate auto-annotation like consensus or conservation graphs\r
- boolean overrideAutoAnnot=false; \r
+ // when true - will add new rows regardless of whether they are duplicate\r
+ // auto-annotation like consensus or conservation graphs\r
+ boolean overrideAutoAnnot = false;\r
if (al.getAlignmentAnnotation() != null)\r
{\r
existingAnnotations = al.getAlignmentAnnotation().length;\r
- if (existingAnnotations>0)\r
+ if (existingAnnotations > 0)\r
{\r
AlignmentAnnotation[] aa = al.getAlignmentAnnotation();\r
- for (int aai=0;aai<aa.length;aai++)\r
+ for (int aai = 0; aai < aa.length; aai++)\r
{\r
if (aa[aai].autoCalculated)\r
{\r
// make a note of the name and description\r
- autoAnnots.put(aa[aai].graph+"\t"+aa[aai].label+"\t"+aa[aai].description+"\t"+(aa[aai].sequenceRef!=null ? aa[aai].sequenceRef.getDisplayId(true) : "")\r
- ,new Integer(1));\r
+ autoAnnots.put(aa[aai].graph\r
+ + "\t"\r
+ + aa[aai].label\r
+ + "\t"\r
+ + aa[aai].description\r
+ + "\t"\r
+ + (aa[aai].sequenceRef != null ? aa[aai].sequenceRef\r
+ .getDisplayId(true) : ""), new Integer(1));\r
}\r
}\r
}\r
}\r
continue;\r
}\r
-\r
+ else if (token.equalsIgnoreCase("GROUP_REF"))\r
+ {\r
+ // Group references could be forward or backwards, so they are\r
+ // resolved after the whole file is read in\r
+ groupRef = null;\r
+ if (st.hasMoreTokens())\r
+ {\r
+ groupRef = st.nextToken();\r
+ if (groupRef.length() < 1)\r
+ {\r
+ groupRef = null; // empty string\r
+ }\r
+ else\r
+ {\r
+ if (groupRefRows.get(groupRef) == null)\r
+ {\r
+ groupRefRows.put(groupRef, new Vector());\r
+ }\r
+ }\r
+ }\r
+ continue;\r
+ }\r
else if (token.equalsIgnoreCase("SEQUENCE_GROUP"))\r
{\r
addGroup(al, st);\r
continue;\r
}\r
\r
+ // Parse out the annotation row\r
graphStyle = AlignmentAnnotation.getGraphValueFromString(token);\r
label = st.nextToken();\r
\r
}\r
\r
}\r
- \r
+\r
annotation = new AlignmentAnnotation(label, description,\r
(index == 0) ? null : annotations, 0, 0, graphStyle);\r
\r
annotation.score = score;\r
- if (!overrideAutoAnnot && autoAnnots.containsKey(annotation.graph+"\t"+annotation.label+"\t"+annotation.description+"\t"+(refSeq!=null ? refSeq.getDisplayId(true) : "")))\r
+ if (!overrideAutoAnnot\r
+ && autoAnnots\r
+ .containsKey(annotation.graph\r
+ + "\t"\r
+ + annotation.label\r
+ + "\t"\r
+ + annotation.description\r
+ + "\t"\r
+ + (refSeq != null ? refSeq\r
+ .getDisplayId(true) : "")))\r
{\r
// skip - we've already got an automatic annotation of this type.\r
continue;\r
// otherwise add it!\r
if (refSeq != null)\r
{\r
- \r
+\r
annotation.belowAlignment = false;\r
// make a copy of refSeq so we can find other matches in the alignment\r
SequenceI referedSeq = refSeq;\r
al.setAnnotationIndex(annotation,\r
al.getAlignmentAnnotation().length\r
- existingAnnotations - 1);\r
+ if (groupRef != null)\r
+ {\r
+ ((Vector) groupRefRows.get(groupRef)).addElement(annotation);\r
+ }\r
// and recover our virgin copy to use again if necessary.\r
annotation = ann;\r
\r
al.setAnnotationIndex(annotation,\r
al.getAlignmentAnnotation().length - existingAnnotations\r
- 1);\r
+ if (groupRef != null)\r
+ {\r
+ ((Vector) groupRefRows.get(groupRef)).addElement(annotation);\r
+ }\r
}\r
}\r
+ // Finally, resolve the groupRefs\r
+ Enumeration en = groupRefRows.keys();\r
+ SequenceGroup theGroup = null;\r
\r
+ while (en.hasMoreElements())\r
+ {\r
+ groupRef = (String) en.nextElement();\r
+ boolean matched = false;\r
+ // Resolve group: TODO: add a getGroupByName method to alignments\r
+ Vector grps = al.getGroups();\r
+ for (int g = 0, gSize = grps.size(); g < gSize; g++)\r
+ {\r
+ theGroup = (SequenceGroup) grps.elementAt(g);\r
+ if (theGroup.getName().equals(groupRef))\r
+ {\r
+ if (matched)\r
+ {\r
+ // TODO: specify and implement duplication of alignment annotation for multiple group references.\r
+ System.err\r
+ .println("Ignoring 1:many group reference mappings for group name '"\r
+ + groupRef+"'");\r
+ }\r
+ else\r
+ {\r
+ matched = true;\r
+ Vector rowset = (Vector) groupRefRows.get(groupRef);\r
+ if (rowset != null && rowset.size() > 0)\r
+ {\r
+ AlignmentAnnotation alan = null;\r
+ for (int elm = 0, elmSize = rowset.size(); elm < elmSize; elm++)\r
+ {\r
+ alan = (AlignmentAnnotation) rowset.elementAt(elm);\r
+ alan.groupRef = theGroup;\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ ((Vector) groupRefRows.get(groupRef)).removeAllElements();\r
+ }\r
} catch (Exception ex)\r
{\r
ex.printStackTrace();\r
\r
Annotation parseAnnotation(String string, int graphStyle)\r
{\r
- boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH); // don't do the glyph test if we don't want secondary structure\r
+ boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH); // don't\r
+ // do the\r
+ // glyph\r
+ // test\r
+ // if we\r
+ // don't\r
+ // want\r
+ // secondary\r
+ // structure\r
String desc = null, displayChar = null;\r
char ss = ' '; // secondaryStructure\r
float value = 0;\r
UserColourScheme ucs = new UserColourScheme();\r
\r
colour = ucs.getColourFromString(string.substring(i + 1, j));\r
- if ( i>0 && string.charAt(i-1)==',')\r
+ if (i > 0 && string.charAt(i - 1) == ',')\r
{\r
// clip the preceding comma as well\r
i--;\r
\r
StringTokenizer st = new StringTokenizer(string, ",", true);\r
String token;\r
- boolean seenContent=false;\r
- int pass=0;\r
+ boolean seenContent = false;\r
+ int pass = 0;\r
while (st.hasMoreTokens())\r
{\r
pass++;\r
}\r
seenContent = false;\r
continue;\r
- } else {\r
+ }\r
+ else\r
+ {\r
seenContent = true;\r
}\r
\r
{\r
try\r
{\r
- displayChar = token; \r
+ displayChar = token;\r
// foo\r
value = new Float(token).floatValue();\r
parsedValue = true;\r
} catch (NumberFormatException ex)\r
{\r
}\r
- } else {\r
- if (token.length()==1)\r
+ }\r
+ else\r
+ {\r
+ if (token.length() == 1)\r
{\r
displayChar = token;\r
}\r
}\r
- if (hasSymbols && (token.equals("H") || token.equals("E") || token.equals(" ")))\r
+ if (hasSymbols\r
+ && (token.equals("H") || token.equals("E") || token\r
+ .equals(" ")))\r
{\r
// Either this character represents a helix or sheet\r
// or an integer which can be displayed\r
displayChar = "";\r
}\r
}\r
- else if (desc == null || (parsedValue && pass>2))\r
+ else if (desc == null || (parsedValue && pass > 2))\r
{\r
desc = token;\r
}\r
\r
}\r
-// if (!dcset && string.charAt(string.length() - 1) == ',')\r
-// {\r
-// displayChar = " "; // empty display char symbol.\r
-// }\r
- if (displayChar != null && desc!=null && desc.length()==1) \r
+ // if (!dcset && string.charAt(string.length() - 1) == ',')\r
+ // {\r
+ // displayChar = " "; // empty display char symbol.\r
+ // }\r
+ if (displayChar != null && desc != null && desc.length() == 1)\r
{\r
if (displayChar.length() > 1)\r
{\r
- // switch desc and displayChar - legacy support \r
+ // switch desc and displayChar - legacy support\r
String tmp = displayChar;\r
displayChar = desc;\r
desc = tmp;\r
- } else {\r
- if (displayChar.equals(desc)) {\r
+ }\r
+ else\r
+ {\r
+ if (displayChar.equals(desc))\r
+ {\r
// duplicate label - hangover from the 'robust parser' above\r
desc = null;\r
}\r
\r
void addRowProperties(AlignmentI al, StringTokenizer st)\r
{\r
- String label = st.nextToken(),keyValue,key,value;\r
- boolean scaletofit=false,centerlab=false,showalllabs=false;\r
- while (st.hasMoreTokens()) {\r
- keyValue=st.nextToken();\r
+ String label = st.nextToken(), keyValue, key, value;\r
+ boolean scaletofit = false, centerlab = false, showalllabs = false;\r
+ while (st.hasMoreTokens())\r
+ {\r
+ keyValue = st.nextToken();\r
key = keyValue.substring(0, keyValue.indexOf("="));\r
value = keyValue.substring(keyValue.indexOf("=") + 1);\r
- if (key.equalsIgnoreCase("scaletofit")) {\r
+ if (key.equalsIgnoreCase("scaletofit"))\r
+ {\r
scaletofit = Boolean.valueOf(value).booleanValue();\r
}\r
- if (key.equalsIgnoreCase("showalllabs")) {\r
- showalllabs = Boolean.valueOf(value).booleanValue();\r
- }\r
- if (key.equalsIgnoreCase("centrelabs")) {\r
- centerlab = Boolean.valueOf(value).booleanValue();\r
- }\r
- AlignmentAnnotation[] alr = al.getAlignmentAnnotation(); \r
- for (int i = 0; i < alr.length; i++)\r
+ if (key.equalsIgnoreCase("showalllabs"))\r
+ {\r
+ showalllabs = Boolean.valueOf(value).booleanValue();\r
+ }\r
+ if (key.equalsIgnoreCase("centrelabs"))\r
+ {\r
+ centerlab = Boolean.valueOf(value).booleanValue();\r
+ }\r
+ AlignmentAnnotation[] alr = al.getAlignmentAnnotation();\r
+ for (int i = 0; i < alr.length; i++)\r
+ {\r
+ if (alr[i].label.equalsIgnoreCase(label))\r
{\r
- if (alr[i].label.equalsIgnoreCase(label))\r
- {\r
- alr[i].centreColLabels = centerlab;\r
- alr[i].scaleColLabel = scaletofit;\r
- alr[i].showAllColLabels = showalllabs;\r
- }\r
+ alr[i].centreColLabels = centerlab;\r
+ alr[i].scaleColLabel = scaletofit;\r
+ alr[i].showAllColLabels = showalllabs;\r
}\r
+ }\r
}\r
}\r
+\r
void addProperties(AlignmentI al, StringTokenizer st)\r
{\r
\r
git://source.jalview.org / jalview.git / blobdiff