/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
* \r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
+ * This file is part of Jalview.\r
* \r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
* \r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
*/\r
package jalview.io;\r
\r
\r
public class AnnotationFile\r
{\r
- StringBuffer text = new StringBuffer("JALVIEW_ANNOTATION\n"\r
- + "# Created: " + new java.util.Date() + "\n\n");\r
+ public AnnotationFile()\r
+ {\r
+ init();\r
+ }\r
+\r
+ /**\r
+ * character used to write newlines\r
+ */\r
+ protected String newline = System.getProperty("line.separator");\r
+\r
+ /**\r
+ * set new line string and reset the output buffer\r
+ * \r
+ * @param nl\r
+ */\r
+ public void setNewlineString(String nl)\r
+ {\r
+ newline = nl;\r
+ init();\r
+ }\r
+\r
+ public String getNewlineString()\r
+ {\r
+ return newline;\r
+ }\r
+\r
+ StringBuffer text;\r
+\r
+ private void init()\r
+ {\r
+ text = new StringBuffer("JALVIEW_ANNOTATION"+newline + "# Created: "\r
+ + new java.util.Date() + newline + newline);\r
+ refSeq = null;\r
+ refSeqId = null;\r
+ }\r
\r
/**\r
* convenience method for pre-2.4 feature files which have no view, hidden\r
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
{\r
if (refSeq != null)\r
{\r
- text.append("\nSEQUENCE_REF\tALIGNMENT\n");\r
+ text.append(newline);\r
+ text.append("SEQUENCE_REF\tALIGNMENT");\r
+ text.append(newline);\r
}\r
\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(newline);\r
+ text.append("SEQUENCE_REF\t");\r
+ text.append(refSeq.getName());\r
+ text.append(newline);\r
+ }\r
+ }\r
+ // mark any group references for the row\r
+ if (row.groupRef == null)\r
{\r
- refSeq = row.sequenceRef;\r
- text.append("\nSEQUENCE_REF\t" + refSeq.getName() + "\n");\r
+\r
+ if (refGroup != null)\r
+ {\r
+ text.append(newline);\r
+ text.append("GROUP_REF\tALIGNMENT");\r
+ text.append(newline);\r
+ }\r
+\r
+ refGroup = null;\r
}\r
+ else\r
+ {\r
+ if (refGroup == null || refGroup != row.groupRef)\r
+ {\r
+ refGroup = row.groupRef;\r
+ text.append(newline);\r
+ text.append("GROUP_REF\t");\r
+ text.append(refGroup.getName());\r
+ text.append(newline);\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
\r
if (row.getThreshold() != null)\r
{\r
- graphLine\r
- .append("GRAPHLINE\t"\r
- + row.label\r
- + "\t"\r
- + row.getThreshold().value\r
- + "\t"\r
- + row.getThreshold().label\r
- + "\t"\r
- + jalview.util.Format.getHexString(row\r
- .getThreshold().colour) + "\n");\r
+ graphLine.append("GRAPHLINE\t");\r
+ graphLine.append(row.label);\r
+ graphLine.append("\t");\r
+ graphLine.append(row.getThreshold().value);\r
+ graphLine.append("\t");\r
+ graphLine.append(row.getThreshold().label);\r
+ graphLine.append("\t");\r
+ graphLine.append(jalview.util.Format.getHexString(row\r
+ .getThreshold().colour));\r
+ graphLine.append(newline);\r
}\r
\r
if (row.graphGroup > -1)\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
if (row.hasScore())\r
text.append("\t" + row.score);\r
\r
- text.append("\n");\r
+ text.append(newline);\r
\r
if (color != null && color != java.awt.Color.black && oneColour)\r
{\r
- colours.append("COLOUR\t" + row.label + "\t"\r
- + jalview.util.Format.getHexString(color) + "\n");\r
+ colours.append("COLOUR\t");\r
+ colours.append(row.label);\r
+ colours.append("\t");\r
+ colours.append(jalview.util.Format.getHexString(color));\r
+ colours.append(newline);\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("\n");\r
+ rowprops.append("ROWPROPERTIES\t");\r
+ rowprops.append(row.label);\r
+ rowprops.append("\tscaletofit=");\r
+ rowprops.append(row.scaleColLabel);\r
+ rowprops.append("\tshowalllabs=");\r
+ rowprops.append(row.showAllColLabels);\r
+ rowprops.append("\tcentrelabs=");\r
+ rowprops.append(row.centreColLabels);\r
+ rowprops.append(newline);\r
}\r
}\r
\r
- text.append("\n");\r
+ text.append(newline);\r
\r
text.append(colours.toString());\r
text.append(graphLine.toString());\r
Enumeration en = graphGroup.elements();\r
while (en.hasMoreElements())\r
{\r
- text.append(en.nextElement() + "\n");\r
+ text.append(en.nextElement());\r
+ text.append(newline);\r
}\r
}\r
text.append(rowprops.toString());\r
\r
if (properties != null)\r
{\r
- text.append("\n\nALIGNMENT");\r
+ text.append(newline);\r
+ text.append(newline);\r
+ text.append("ALIGNMENT");\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
+ text.append("\t");\r
+ text.append(key);\r
+ text.append("=");\r
+ text.append(properties.get(key));\r
}\r
// TODO: output alignment visualization settings here if required\r
\r
else\r
{\r
seqrep = sg.getSeqrep();\r
- text.append("SEQUENCE_REF\t" + seqrep.getName() + "\n");\r
- text.append("SEQUENCE_GROUP\t" + sg.getName() + "\t"\r
- + (seqrep.findPosition(sg.getStartRes())) + "\t"\r
- + (seqrep.findPosition(sg.getEndRes())) + "\t" + "-1\t");\r
+ text.append("SEQUENCE_REF\t");\r
+ text.append(seqrep.getName());\r
+ text.append(newline);\r
+ text.append("SEQUENCE_GROUP\t");\r
+ text.append(sg.getName());\r
+ text.append("\t");\r
+ text.append((seqrep.findPosition(sg.getStartRes())));\r
+ text.append("\t");\r
+ text.append((seqrep.findPosition(sg.getEndRes())));\r
+ text.append("\t");\r
+ text.append("-1\t");\r
}\r
for (int s = 0; s < sg.getSize(); s++)\r
{\r
- text.append(sg.getSequenceAt(s).getName() + "\t");\r
+ text.append(sg.getSequenceAt(s).getName());\r
+ text.append("\t");\r
}\r
-\r
- text.append("\nPROPERTIES\t" + sg.getName() + "\t");\r
+ text.append(newline);\r
+ text.append("PROPERTIES\t");\r
+ text.append(sg.getName());\r
+ text.append("\t");\r
\r
if (sg.getDescription() != null)\r
{\r
- text.append("description=" + sg.getDescription() + "\t");\r
+ text.append("description=");\r
+ text.append(sg.getDescription());\r
+ text.append("\t");\r
}\r
if (sg.cs != null)\r
{\r
- text.append("colour=" + ColourSchemeProperty.getColourName(sg.cs)\r
- + "\t");\r
+ text.append("colour=");\r
+ text.append(ColourSchemeProperty.getColourName(sg.cs));\r
+ text.append("\t");\r
if (sg.cs.getThreshold() != 0)\r
{\r
- text.append("pidThreshold=" + sg.cs.getThreshold());\r
+ text.append("pidThreshold=");\r
+ text.append(sg.cs.getThreshold());\r
}\r
if (sg.cs.conservationApplied())\r
{\r
- text.append("consThreshold=" + sg.cs.getConservationInc() + "\t");\r
+ text.append("consThreshold=");\r
+ text.append(sg.cs.getConservationInc());\r
+ text.append("\t");\r
}\r
}\r
- text.append("outlineColour="\r
- + jalview.util.Format.getHexString(sg.getOutlineColour())\r
- + "\t");\r
-\r
- text.append("displayBoxes=" + sg.getDisplayBoxes() + "\t");\r
- text.append("displayText=" + sg.getDisplayText() + "\t");\r
- text.append("colourText=" + sg.getColourText() + "\t");\r
- text.append("showUnconserved=" + sg.getShowunconserved() + "\t");\r
+ text.append("outlineColour=");\r
+ text.append(jalview.util.Format.getHexString(sg.getOutlineColour()));\r
+ text.append("\t");\r
+\r
+ text.append("displayBoxes=");\r
+ text.append(sg.getDisplayBoxes());\r
+ text.append("\t");\r
+ text.append("displayText=");\r
+ text.append(sg.getDisplayText());\r
+ text.append("\t");\r
+ text.append("colourText=");\r
+ text.append(sg.getColourText());\r
+ text.append("\t");\r
+ text.append("showUnconserved=");\r
+ text.append(sg.getShowNonconserved());\r
+ text.append("\t");\r
if (sg.textColour != java.awt.Color.black)\r
{\r
- text.append("textCol1="\r
- + jalview.util.Format.getHexString(sg.textColour) + "\t");\r
+ text.append("textCol1=");\r
+ text.append(jalview.util.Format.getHexString(sg.textColour));\r
+ text.append("\t");\r
}\r
if (sg.textColour2 != java.awt.Color.white)\r
{\r
- text.append("textCol2="\r
- + jalview.util.Format.getHexString(sg.textColour2) + "\t");\r
+ text.append("textCol2=");\r
+ text.append(jalview.util.Format.getHexString(sg.textColour2));\r
+ text.append("\t");\r
}\r
if (sg.thresholdTextColour != 0)\r
{\r
- text.append("textColThreshold=" + sg.thresholdTextColour + "\t");\r
+ text.append("textColThreshold=");\r
+ text.append(sg.thresholdTextColour);\r
+ text.append("\t");\r
}\r
if (sg.idColour != null)\r
{\r
- text.append("idColour="\r
- + jalview.util.Format.getHexString(sg.idColour) + "\t");\r
+ text.append("idColour=");\r
+ text.append(jalview.util.Format.getHexString(sg.idColour));\r
+ text.append("\t");\r
}\r
if (sg.isHidereps())\r
{\r
if (seqrep != null)\r
{\r
// terminate the last line and clear the sequence ref for the group\r
- text.append("\nSEQUENCE_REF");\r
+ text.append(newline);\r
+ text.append("SEQUENCE_REF");\r
}\r
- text.append("\n\n");\r
+ text.append(newline);\r
+ text.append(newline);\r
\r
}\r
}\r
public boolean readAnnotationFile(AlignmentI al, String file,\r
String protocol)\r
{\r
- Hashtable autoAnnots=new Hashtable();\r
+ BufferedReader in = null;\r
try\r
{\r
- BufferedReader in = null;\r
if (protocol.equals(AppletFormatAdapter.FILE))\r
{\r
in = new BufferedReader(new FileReader(file));\r
in = new BufferedReader(new java.io.InputStreamReader(is));\r
}\r
}\r
+ if (in != null)\r
+ {\r
+ return parseAnnotationFrom(al, in);\r
+ }\r
+\r
+ } catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ System.out.println("Problem reading annotation file: " + ex);\r
+ return false;\r
+ }\r
+ return false;\r
+ }\r
+\r
+ public boolean parseAnnotationFrom(AlignmentI al, BufferedReader in)\r
+ throws Exception\r
+ {\r
+ boolean modified = false;\r
+ String groupRef = null;\r
+ Hashtable groupRefRows = new Hashtable();\r
\r
+ Hashtable autoAnnots = new Hashtable();\r
+ {\r
String line, label, description, token;\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(\r
+ autoAnnotsKey(aa[aai], aa[aai].sequenceRef,\r
+ (aa[aai].groupRef == null ? null\r
+ : aa[aai].groupRef.getName())),\r
+ new Integer(1));\r
}\r
}\r
}\r
{\r
// TODO: use graduated colour def'n here too\r
colourAnnotations(al, st.nextToken(), st.nextToken());\r
+ modified = true;\r
continue;\r
}\r
\r
else if (token.equalsIgnoreCase("COMBINE"))\r
{\r
combineAnnotations(al, st);\r
+ modified = true;\r
continue;\r
}\r
else if (token.equalsIgnoreCase("ROWPROPERTIES"))\r
{\r
addRowProperties(al, st);\r
+ modified = true;\r
continue;\r
}\r
else if (token.equalsIgnoreCase("GRAPHLINE"))\r
{\r
addLine(al, st);\r
+ modified = true;\r
continue;\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
else if (token.equalsIgnoreCase("PROPERTIES"))\r
{\r
addProperties(al, st);\r
+ modified = true;\r
continue;\r
}\r
\r
else if (token.equalsIgnoreCase("BELOW_ALIGNMENT"))\r
{\r
setBelowAlignment(al, st);\r
+ modified = true;\r
continue;\r
}\r
else if (token.equalsIgnoreCase("ALIGNMENT"))\r
{\r
addAlignmentDetails(al, st);\r
+ modified = true;\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.containsKey(autoAnnotsKey(annotation, refSeq,\r
+ groupRef)))\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
+ // and set modification flag\r
+ modified = true;\r
}\r
+ // Finally, resolve the groupRefs\r
+ Enumeration en = groupRefRows.keys();\r
+ SequenceGroup theGroup = null;\r
\r
- } catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- System.out.println("Problem reading annotation file: " + ex);\r
- return false;\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\r
+ // 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
}\r
- return true;\r
+ return modified;\r
+ }\r
+\r
+ private Object autoAnnotsKey(AlignmentAnnotation annotation,\r
+ SequenceI refSeq, String groupRef)\r
+ {\r
+ return annotation.graph + "\t" + annotation.label + "\t"\r
+ + annotation.description + "\t"\r
+ + (refSeq != null ? refSeq.getDisplayId(true) : "");\r
}\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.equals("S") || 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
int graphGroup = -1;\r
String group = st.nextToken();\r
// First make sure we are not overwriting the graphIndex\r
- for (int i = 0; i < al.getAlignmentAnnotation().length; i++)\r
+ if (al.getAlignmentAnnotation() != null)\r
{\r
- if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))\r
- {\r
- graphGroup = al.getAlignmentAnnotation()[i].graphGroup + 1;\r
- al.getAlignmentAnnotation()[i].graphGroup = graphGroup;\r
- break;\r
- }\r
- }\r
-\r
- // Now update groups\r
- while (st.hasMoreTokens())\r
- {\r
- group = st.nextToken();\r
for (int i = 0; i < al.getAlignmentAnnotation().length; i++)\r
{\r
if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))\r
{\r
+ graphGroup = al.getAlignmentAnnotation()[i].graphGroup + 1;\r
al.getAlignmentAnnotation()[i].graphGroup = graphGroup;\r
break;\r
}\r
}\r
+\r
+ // Now update groups\r
+ while (st.hasMoreTokens())\r
+ {\r
+ group = st.nextToken();\r
+ for (int i = 0; i < al.getAlignmentAnnotation().length; i++)\r
+ {\r
+ if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))\r
+ {\r
+ al.getAlignmentAnnotation()[i].graphGroup = graphGroup;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ System.err\r
+ .println("Couldn't combine annotations. None are added to alignment yet!");\r
}\r
}\r
\r
void addLine(AlignmentI al, StringTokenizer st)\r
{\r
String group = st.nextToken();\r
- AlignmentAnnotation annotation = null;\r
-\r
- for (int i = 0; i < al.getAlignmentAnnotation().length; i++)\r
+ AlignmentAnnotation annotation = null, alannot[] = al\r
+ .getAlignmentAnnotation();\r
+ if (alannot != null)\r
{\r
- if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))\r
+ for (int i = 0; i < alannot.length; i++)\r
{\r
- annotation = al.getAlignmentAnnotation()[i];\r
- break;\r
+ if (alannot[i].label.equalsIgnoreCase(group))\r
+ {\r
+ annotation = alannot[i];\r
+ break;\r
+ }\r
}\r
}\r
-\r
if (annotation == null)\r
{\r
return;\r
}\r
else\r
{\r
- sg\r
- .addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1),\r
- false);\r
+ sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1), false);\r
}\r
}\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
+ 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
+ if (alr != null)\r
+ {\r
for (int i = 0; i < alr.length; i++)\r
{\r
if (alr[i].label.equalsIgnoreCase(label))\r
alr[i].showAllColLabels = showalllabs;\r
}\r
}\r
+ }\r
}\r
}\r
+\r
void addProperties(AlignmentI al, StringTokenizer st)\r
{\r
\r
{\r
sg.cs.setConservationInc(Integer.parseInt(value));\r
Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3, sg.getSequences(null), sg\r
- .getStartRes(), sg.getEndRes() + 1);\r
+ ResidueProperties.propHash, 3, sg.getSequences(null),\r
+ sg.getStartRes(), sg.getEndRes() + 1);\r
\r
c.calculate();\r
c.verdict(false, 25);\r
}\r
else if (key.equalsIgnoreCase("showUnconserved"))\r
{\r
- sg.setShowunconserved(Boolean.valueOf(value).booleanValue());\r
+ sg.setShowNonconserved(Boolean.valueOf(value).booleanValue());\r
}\r
else if (key.equalsIgnoreCase("displayText"))\r
{\r
void setBelowAlignment(AlignmentI al, StringTokenizer st)\r
{\r
String token;\r
- AlignmentAnnotation aa;\r
+ AlignmentAnnotation aa, ala[] = al.getAlignmentAnnotation();\r
+ if (ala == null)\r
+ {\r
+ System.err\r
+ .print("Warning - no annotation to set below for sequence associated annotation:");\r
+ }\r
while (st.hasMoreTokens())\r
{\r
token = st.nextToken();\r
- for (int i = 0; i < al.getAlignmentAnnotation().length; i++)\r
+ if (ala == null)\r
+ {\r
+ System.err.print(" " + token);\r
+ }\r
+ else\r
{\r
- aa = al.getAlignmentAnnotation()[i];\r
- if (aa.sequenceRef == refSeq && aa.label.equals(token))\r
+ for (int i = 0; i < al.getAlignmentAnnotation().length; i++)\r
{\r
- aa.belowAlignment = true;\r
+ aa = al.getAlignmentAnnotation()[i];\r
+ if (aa.sequenceRef == refSeq && aa.label.equals(token))\r
+ {\r
+ aa.belowAlignment = true;\r
+ }\r
}\r
}\r
}\r
+ if (ala == null)\r
+ {\r
+ System.err.print("\n");\r
+ }\r
}\r
\r
void addAlignmentDetails(AlignmentI al, StringTokenizer st)\r
else\r
{\r
sp.append(atos.substring(p));\r
- sp.append("\n");\r
+ sp.append(newline);\r
}\r
p = cp + 1;\r
} while (p > 0);\r
git://source.jalview.org / jalview.git / blobdiff