-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, 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
- *\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
- *\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
- */\r
-\r
-package jalview.io;\r
-\r
-import java.io.*;\r
-import jalview.datamodel.*;\r
-import java.util.*;\r
-import jalview.schemes.UserColourScheme;\r
-import java.net.URL;\r
-\r
-\r
-public class AnnotationFile\r
-{\r
-\r
- public String printAnnotations(AlignmentAnnotation [] annotations)\r
- {\r
- StringBuffer text = new StringBuffer(\r
- "JALVIEW_ANNOTATION\n"\r
- +"# Created: "\r
- +new java.util.Date()+"\n\n");\r
-\r
- AlignmentAnnotation row;\r
- String comma;\r
- String seqref = null;\r
-\r
- StringBuffer colours = new StringBuffer();\r
- StringBuffer graphLine = new StringBuffer();\r
-\r
- Hashtable graphGroup = new Hashtable();\r
-\r
- java.awt.Color color;\r
-\r
- for(int i=0; i<annotations.length; i++)\r
- {\r
- row = annotations[i];\r
- color = null;\r
-\r
- if( row.sequenceRef == null)\r
- seqref = null;\r
-\r
- else if (seqref == null\r
- || !seqref.equals(row.sequenceRef.getName()))\r
- {\r
- seqref = row.sequenceRef.getName();\r
- text.append("\nSEQUENCE_REF\t" + seqref + "\n");\r
- }\r
-\r
-\r
- switch( row.graph )\r
- {\r
- case AlignmentAnnotation.NO_GRAPH:\r
- text.append("NO_GRAPH\t");\r
- break;\r
- case AlignmentAnnotation.BAR_GRAPH:\r
- text.append("BAR_GRAPH\t");\r
- case AlignmentAnnotation.LINE_GRAPH:\r
- text.append("LINE_GRAPH\t");\r
-\r
- if(row.getThreshold()!=null)\r
- graphLine.append("GRAPHLINE\t"\r
- + row.label + "\t"\r
- + row.getThreshold().value + "\t"\r
- + row.getThreshold().label + "\t"\r
- + jalview.util.Format.getHexString(\r
- row.getThreshold().colour)+"\n"\r
- );\r
-\r
- if(row.graphGroup>-1)\r
- {\r
- String key = String.valueOf(row.graphGroup);\r
- if(graphGroup.containsKey(key))\r
- graphGroup.put(key, graphGroup.get(key)\r
- +"\t"+row.label);\r
- else\r
- graphGroup.put(key, row.label);\r
- }\r
- }\r
-\r
- text.append(row.label+"\t");\r
-\r
- for(int j=0; j<row.annotations.length; j++)\r
- {\r
- if(row.annotations[j]!=null)\r
- {\r
- comma = "";\r
- if (row.annotations[j].displayCharacter.length() > 0\r
- && !row.annotations[j].displayCharacter.equals(" "))\r
- {\r
- text.append(row.annotations[j].displayCharacter);\r
- comma = ",";\r
- }\r
- if (row.annotations[j].secondaryStructure!=' ')\r
- {\r
- text.append(comma + row.annotations[j].secondaryStructure);\r
- comma = ",";\r
- }\r
- if (row.annotations[j].value!=0f)\r
- {\r
- color = row.annotations[j].colour;\r
- text.append(comma + row.annotations[j].value);\r
- }\r
- }\r
- text.append("|");\r
- }\r
-\r
- text.append("\n");\r
-\r
- if(color!=null && color!=java.awt.Color.black)\r
- {\r
- colours.append("COLOUR\t"\r
- +row.label+"\t"\r
- +jalview.util.Format.getHexString(color)+"\n");\r
- }\r
-\r
- }\r
-\r
- text.append("\n");\r
-\r
- text.append(colours.toString());\r
- text.append(graphLine.toString());\r
- if(graphGroup.size()>0)\r
- {\r
- text.append("COMBINE\t");\r
- Enumeration en = graphGroup.elements();\r
- while(en.hasMoreElements())\r
- {\r
- text.append(en.nextElement()+"\n");\r
- }\r
- }\r
-\r
- return text.toString();\r
- }\r
-\r
- public boolean readAnnotationFile(AlignmentI al, String file)\r
- {\r
- try\r
- {\r
- BufferedReader in = null;\r
- java.io.InputStream is = getClass().getResourceAsStream("/" + file);\r
- if (is != null)\r
- {\r
- in = new BufferedReader(new java.io.InputStreamReader(is));\r
- }\r
- else\r
- {\r
- try\r
- {\r
- URL url = new URL(file);\r
- in = new BufferedReader(new InputStreamReader(url.openStream()));\r
- }\r
- catch (java.net.MalformedURLException ex)\r
- {\r
- in = new BufferedReader(new FileReader(file));\r
- }\r
- }\r
-\r
- String line, label, description, token;\r
- int graphStyle, index;\r
- SequenceI refSeq = null;\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
- AlignmentAnnotation annotation = null;\r
-\r
- // First confirm this is an Annotation file\r
- boolean jvAnnotationFile = false;\r
- while ( (line = in.readLine()) != null)\r
- {\r
- if (line.indexOf("#") == 0 )\r
- continue;\r
-\r
- if (line.indexOf("JALVIEW_ANNOTATION") > -1)\r
- {\r
- jvAnnotationFile = true;\r
- break;\r
- }\r
- }\r
-\r
- if(!jvAnnotationFile)\r
- {\r
- in.close();\r
- return false;\r
- }\r
-\r
- while ( (line = in.readLine()) != null)\r
- {\r
- if(line.indexOf("#")==0\r
- || line.indexOf("JALVIEW_ANNOTATION")>-1\r
- || line.length()==0)\r
- continue;\r
-\r
- st = new StringTokenizer(line, "\t");\r
- token = st.nextToken();\r
- if(token.equalsIgnoreCase("COLOUR"))\r
- {\r
- colourAnnotations(al, st.nextToken(), st.nextToken());\r
- continue;\r
- }\r
-\r
- if(token.equalsIgnoreCase("COMBINE") )\r
- {\r
- combineAnnotations(al, st);\r
- continue;\r
- }\r
-\r
- if (token.equalsIgnoreCase("GRAPHLINE"))\r
- {\r
- addLine(al, st);\r
- continue;\r
- }\r
-\r
-\r
- if(token.equalsIgnoreCase("SEQUENCE_REF") )\r
- {\r
- refSeq = al.findName(st.nextToken());\r
- try{\r
- refSeqIndex = Integer.parseInt(st.nextToken());\r
- }\r
- catch(Exception ex)\r
- {\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[alWidth];\r
-\r
- index = 0;\r
- boolean emptyColumn = true;\r
-\r
-\r
- while (st.hasMoreElements() && index<alWidth)\r
- {\r
- token = st.nextToken().trim();\r
- if(token.equals("|"))\r
- {\r
- if(emptyColumn)\r
- index++;\r
-\r
- emptyColumn = true;\r
- }\r
- else\r
- {\r
- annotations[index++] = parseAnnotation(token);\r
- emptyColumn = false;\r
- }\r
- }\r
-\r
- annotation = new AlignmentAnnotation(label,\r
- description,\r
- annotations,\r
- 0,\r
- 0,\r
- graphStyle);\r
-\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
- {\r
- ex.printStackTrace();\r
- System.out.println("Problem reading annotation file: "+ex);\r
- return false;\r
- }\r
- return true;\r
- }\r
-\r
- Annotation parseAnnotation(String string)\r
- {\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
- {\r
- token = st.nextToken().trim();\r
- if(token.length()==0)\r
- continue;\r
-\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.equals("H") || token.equals("E"))\r
- {\r
- // Either this character represents a helix or sheet\r
- // or an integer which can be displayed\r
- ss = token.charAt(0);\r
- }\r
- else if(desc.length()<1)\r
- desc = token;\r
-\r
- }\r
-\r
- return new Annotation(displayChar, desc, ss, value);\r
- }\r
-\r
- void colourAnnotations(AlignmentI al, String label, String colour)\r
- {\r
- UserColourScheme ucs = new UserColourScheme(colour);\r
- Annotation[] annotations;\r
- for(int i=0; i<al.getAlignmentAnnotation().length; i++)\r
- {\r
- if(al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(label))\r
- {\r
- annotations = al.getAlignmentAnnotation()[i].annotations;\r
- for(int j=0; j<annotations.length; j++)\r
- {\r
- if(annotations[j]!=null)\r
- annotations[j].colour = ucs.findColour("A");\r
- }\r
- }\r
- }\r
- }\r
-\r
- void combineAnnotations(AlignmentI al, StringTokenizer st)\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
- {\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
-\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
- {\r
- if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))\r
- {\r
- annotation = al.getAlignmentAnnotation()[i];\r
- break;\r
- }\r
- }\r
-\r
- if(annotation==null)\r
- return;\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
- {\r
- UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
- colour = ucs.findColour("A");\r
- }\r
-\r
- annotation.setThreshold(new GraphLine(value, label, colour));\r
-\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+import java.io.*;
+import java.net.*;
+import java.util.*;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.schemes.*;
+
+public class AnnotationFile
+{
+ public AnnotationFile()
+ {
+ init();
+ }
+
+ /**
+ * character used to write newlines
+ */
+ protected String newline = System.getProperty("line.separator");
+
+ /**
+ * set new line string and reset the output buffer
+ *
+ * @param nl
+ */
+ public void setNewlineString(String nl)
+ {
+ newline = nl;
+ init();
+ }
+
+ public String getNewlineString()
+ {
+ return newline;
+ }
+
+ StringBuffer text;
+
+ private void init()
+ {
+ text = new StringBuffer("JALVIEW_ANNOTATION" + newline + "# Created: "
+ + new java.util.Date() + newline + newline);
+ refSeq = null;
+ refSeqId = null;
+ }
+
+ /**
+ * convenience method for pre-2.4 feature files which have no view, hidden
+ * columns or hidden row keywords.
+ *
+ * @param annotations
+ * @param list
+ * @param properties
+ * @return feature file as a string.
+ */
+ public String printAnnotations(AlignmentAnnotation[] annotations,
+ List<SequenceGroup> list, Hashtable properties)
+ {
+ return printAnnotations(annotations, list, properties, null);
+
+ }
+
+ /**
+ * hold all the information about a particular view definition read from or
+ * written out in an annotations file.
+ */
+ public class ViewDef
+ {
+ public String viewname;
+
+ public HiddenSequences hidseqs;
+
+ public ColumnSelection hiddencols;
+
+ public Vector visibleGroups;
+
+ public Hashtable hiddenRepSeqs;
+
+ public ViewDef(String viewname, HiddenSequences hidseqs,
+ ColumnSelection hiddencols, Hashtable hiddenRepSeqs)
+ {
+ this.viewname = viewname;
+ this.hidseqs = hidseqs;
+ this.hiddencols = hiddencols;
+ this.hiddenRepSeqs = hiddenRepSeqs;
+ }
+ }
+
+ /**
+ * Prepare an annotation file given a set of annotations, groups, alignment
+ * properties and views.
+ *
+ * @param annotations
+ * @param list
+ * @param properties
+ * @param views
+ * @return annotation file
+ */
+ public String printAnnotations(AlignmentAnnotation[] annotations,
+ List<SequenceGroup> list, Hashtable properties, ViewDef[] views)
+ {
+ // TODO: resolve views issue : annotationFile could contain visible region,
+ // or full data + hidden region specifications for a view.
+ if (annotations != null)
+ {
+ boolean oneColour = true;
+ AlignmentAnnotation row;
+ String comma;
+ SequenceI refSeq = null;
+ SequenceGroup refGroup = null;
+
+ StringBuffer colours = new StringBuffer();
+ StringBuffer graphLine = new StringBuffer();
+ StringBuffer rowprops = new StringBuffer();
+ Hashtable<Integer, String> graphGroup = new Hashtable<Integer, String>();
+ Hashtable<Integer, Object[]> graphGroup_refs = new Hashtable<Integer, Object[]>();
+ BitSet graphGroupSeen = new BitSet();
+
+ java.awt.Color color;
+
+ for (int i = 0; i < annotations.length; i++)
+ {
+ row = annotations[i];
+
+ if (!row.visible
+ && !row.hasScore()
+ && !(row.graphGroup > -1 && graphGroupSeen
+ .get(row.graphGroup)))
+ {
+ continue;
+ }
+
+ color = null;
+ oneColour = true;
+
+ // mark any sequence references for the row
+ writeSequence_Ref(refSeq, row.sequenceRef);
+ refSeq = row.sequenceRef;
+ // mark any group references for the row
+ writeGroup_Ref(refGroup, row.groupRef);
+ refGroup = row.groupRef;
+
+ boolean hasGlyphs = row.hasIcons, hasLabels = row.hasText, hasValues = row.hasScore, hasText = false;
+ // lookahead to check what the annotation row object actually contains.
+ for (int j = 0; row.annotations != null
+ && j < row.annotations.length
+ && (!hasGlyphs || !hasLabels || !hasValues); j++)
+ {
+ if (row.annotations[j] != null)
+ {
+ hasLabels |= (row.annotations[j].displayCharacter != null
+ && row.annotations[j].displayCharacter.length() > 0 && !row.annotations[j].displayCharacter
+ .equals(" "));
+ hasGlyphs |= (row.annotations[j].secondaryStructure != 0 && row.annotations[j].secondaryStructure != ' ');
+ hasValues |= (row.annotations[j].value != Float.NaN); // NaNs can't
+ // be
+ // rendered..
+ hasText |= (row.annotations[j].description != null && row.annotations[j].description
+ .length() > 0);
+ }
+ }
+
+ if (row.graph == AlignmentAnnotation.NO_GRAPH)
+ {
+ text.append("NO_GRAPH\t");
+ hasValues = false; // only secondary structure
+ // hasLabels = false; // and annotation description string.
+ }
+ else
+ {
+ if (row.graph == AlignmentAnnotation.BAR_GRAPH)
+ {
+ text.append("BAR_GRAPH\t");
+ hasGlyphs = false; // no secondary structure
+
+ }
+ else if (row.graph == AlignmentAnnotation.LINE_GRAPH)
+ {
+ hasGlyphs = false; // no secondary structure
+ text.append("LINE_GRAPH\t");
+ }
+
+ if (row.getThreshold() != null)
+ {
+ graphLine.append("GRAPHLINE\t");
+ graphLine.append(row.label);
+ graphLine.append("\t");
+ graphLine.append(row.getThreshold().value);
+ graphLine.append("\t");
+ graphLine.append(row.getThreshold().label);
+ graphLine.append("\t");
+ graphLine.append(jalview.util.Format.getHexString(row
+ .getThreshold().colour));
+ graphLine.append(newline);
+ }
+
+ if (row.graphGroup > -1)
+ {
+ graphGroupSeen.set(row.graphGroup);
+ Integer key = new Integer(row.graphGroup);
+ if (graphGroup.containsKey(key))
+ {
+ graphGroup.put(key, graphGroup.get(key) + "\t" + row.label);
+
+ }
+ else
+ {
+ graphGroup_refs.put(key, new Object[]
+ { refSeq, refGroup });
+ graphGroup.put(key, row.label);
+ }
+ }
+ }
+
+ text.append(row.label + "\t");
+ if (row.description != null)
+ {
+ text.append(row.description + "\t");
+ }
+ for (int j = 0; row.annotations != null
+ && j < row.annotations.length; j++)
+ {
+ if (refSeq != null
+ && jalview.util.Comparison.isGap(refSeq.getCharAt(j)))
+ {
+ continue;
+ }
+
+ if (row.annotations[j] != null)
+ {
+ comma = "";
+ if (hasGlyphs) // could be also hasGlyphs || ...
+ {
+
+ text.append(comma);
+ if (row.annotations[j].secondaryStructure != ' ')
+ {
+ // only write out the field if its not whitespace.
+ text.append(row.annotations[j].secondaryStructure);
+ }
+ comma = ",";
+ }
+ if (hasValues)
+ {
+ if (row.annotations[j].value != Float.NaN)
+ {
+ text.append(comma + row.annotations[j].value);
+ }
+ else
+ {
+ System.err.println("Skipping NaN - not valid value.");
+ text.append(comma + 0f);// row.annotations[j].value);
+ }
+ comma = ",";
+ }
+ if (hasLabels)
+ {
+ // TODO: labels are emitted after values for bar graphs.
+ if // empty labels are allowed, so
+ (row.annotations[j].displayCharacter != null
+ && row.annotations[j].displayCharacter.length() > 0
+ && !row.annotations[j].displayCharacter.equals(" "))
+ {
+ text.append(comma + row.annotations[j].displayCharacter);
+ comma = ",";
+ }
+ }
+ if (hasText)
+ {
+ if (row.annotations[j].description != null
+ && row.annotations[j].description.length() > 0
+ && !row.annotations[j].description
+ .equals(row.annotations[j].displayCharacter))
+ {
+ text.append(comma + row.annotations[j].description);
+ comma = ",";
+ }
+ }
+ if (color != null && !color.equals(row.annotations[j].colour))
+ {
+ oneColour = false;
+ }
+
+ color = row.annotations[j].colour;
+
+ if (row.annotations[j].colour != null
+ && row.annotations[j].colour != java.awt.Color.black)
+ {
+ text.append(comma
+ + "["
+ + jalview.util.Format
+ .getHexString(row.annotations[j].colour)
+ + "]");
+ comma = ",";
+ }
+ }
+ text.append("|");
+ }
+
+ if (row.hasScore())
+ text.append("\t" + row.score);
+
+ text.append(newline);
+
+ if (color != null && color != java.awt.Color.black && oneColour)
+ {
+ colours.append("COLOUR\t");
+ colours.append(row.label);
+ colours.append("\t");
+ colours.append(jalview.util.Format.getHexString(color));
+ colours.append(newline);
+ }
+ if (row.scaleColLabel || row.showAllColLabels
+ || row.centreColLabels)
+ {
+ rowprops.append("ROWPROPERTIES\t");
+ rowprops.append(row.label);
+ rowprops.append("\tscaletofit=");
+ rowprops.append(row.scaleColLabel);
+ rowprops.append("\tshowalllabs=");
+ rowprops.append(row.showAllColLabels);
+ rowprops.append("\tcentrelabs=");
+ rowprops.append(row.centreColLabels);
+ rowprops.append(newline);
+ }
+ if (graphLine.length() > 0)
+ {
+ text.append(graphLine.toString());
+ graphLine.setLength(0);
+ }
+ }
+
+ text.append(newline);
+
+ text.append(colours.toString());
+ if (graphGroup.size() > 0)
+ {
+ SequenceI oldRefSeq = refSeq;
+ SequenceGroup oldRefGroup = refGroup;
+ for (Map.Entry<Integer, String> combine_statement : graphGroup
+ .entrySet())
+ {
+ Object[] seqRefAndGroup = graphGroup_refs.get(combine_statement
+ .getKey());
+
+ writeSequence_Ref(refSeq, (SequenceI) seqRefAndGroup[0]);
+ refSeq = (SequenceI) seqRefAndGroup[0];
+
+ writeGroup_Ref(refGroup, (SequenceGroup) seqRefAndGroup[1]);
+ refGroup = (SequenceGroup) seqRefAndGroup[1];
+ text.append("COMBINE\t");
+ text.append(combine_statement.getValue());
+ text.append(newline);
+ }
+ writeSequence_Ref(refSeq, oldRefSeq);
+ refSeq = oldRefSeq;
+
+ writeGroup_Ref(refGroup, oldRefGroup);
+ refGroup = oldRefGroup;
+ }
+ text.append(rowprops.toString());
+ }
+
+ if (list != null)
+ {
+ printGroups(list);
+ }
+
+ if (properties != null)
+ {
+ text.append(newline);
+ text.append(newline);
+ text.append("ALIGNMENT");
+ Enumeration en = properties.keys();
+ while (en.hasMoreElements())
+ {
+ String key = en.nextElement().toString();
+ text.append("\t");
+ text.append(key);
+ text.append("=");
+ text.append(properties.get(key));
+ }
+ // TODO: output alignment visualization settings here if required
+
+ }
+
+ return text.toString();
+ }
+
+ private Object writeGroup_Ref(SequenceGroup refGroup,
+ SequenceGroup next_refGroup)
+ {
+ if (next_refGroup == null)
+ {
+
+ if (refGroup != null)
+ {
+ text.append(newline);
+ text.append("GROUP_REF\t");
+ text.append("ALIGNMENT");
+ text.append(newline);
+ }
+ return true;
+ }
+ else
+ {
+ if (refGroup == null || refGroup != next_refGroup)
+ {
+ text.append(newline);
+ text.append("GROUP_REF\t");
+ text.append(next_refGroup.getName());
+ text.append(newline);
+ return true;
+ }
+ }
+ return false;
+ }
+
+ private boolean writeSequence_Ref(SequenceI refSeq, SequenceI next_refSeq)
+ {
+
+ if (next_refSeq == null)
+ {
+ if (refSeq != null)
+ {
+ text.append(newline);
+ text.append("SEQUENCE_REF\t");
+ text.append("ALIGNMENT");
+ text.append(newline);
+ return true;
+ }
+ }
+ else
+ {
+ if (refSeq == null || refSeq != next_refSeq)
+ {
+ text.append(newline);
+ text.append("SEQUENCE_REF\t");
+ text.append(next_refSeq.getName());
+ text.append(newline);
+ return true;
+ }
+ }
+ return false;
+ }
+
+ public void printGroups(List<SequenceGroup> list)
+ {
+ SequenceI seqrep = null;
+ for (SequenceGroup sg : list)
+ {
+ if (!sg.hasSeqrep())
+ {
+ text.append("SEQUENCE_GROUP\t" + sg.getName() + "\t"
+ + (sg.getStartRes() + 1) + "\t" + (sg.getEndRes() + 1)
+ + "\t" + "-1\t");
+ seqrep = null;
+ }
+ else
+ {
+ seqrep = sg.getSeqrep();
+ text.append("SEQUENCE_REF\t");
+ text.append(seqrep.getName());
+ text.append(newline);
+ text.append("SEQUENCE_GROUP\t");
+ text.append(sg.getName());
+ text.append("\t");
+ text.append((seqrep.findPosition(sg.getStartRes())));
+ text.append("\t");
+ text.append((seqrep.findPosition(sg.getEndRes())));
+ text.append("\t");
+ text.append("-1\t");
+ }
+ for (int s = 0; s < sg.getSize(); s++)
+ {
+ text.append(sg.getSequenceAt(s).getName());
+ text.append("\t");
+ }
+ text.append(newline);
+ text.append("PROPERTIES\t");
+ text.append(sg.getName());
+ text.append("\t");
+
+ if (sg.getDescription() != null)
+ {
+ text.append("description=");
+ text.append(sg.getDescription());
+ text.append("\t");
+ }
+ if (sg.cs != null)
+ {
+ text.append("colour=");
+ text.append(ColourSchemeProperty.getColourName(sg.cs));
+ text.append("\t");
+ if (sg.cs.getThreshold() != 0)
+ {
+ text.append("pidThreshold=");
+ text.append(sg.cs.getThreshold());
+ }
+ if (sg.cs.conservationApplied())
+ {
+ text.append("consThreshold=");
+ text.append(sg.cs.getConservationInc());
+ text.append("\t");
+ }
+ }
+ text.append("outlineColour=");
+ text.append(jalview.util.Format.getHexString(sg.getOutlineColour()));
+ text.append("\t");
+
+ text.append("displayBoxes=");
+ text.append(sg.getDisplayBoxes());
+ text.append("\t");
+ text.append("displayText=");
+ text.append(sg.getDisplayText());
+ text.append("\t");
+ text.append("colourText=");
+ text.append(sg.getColourText());
+ text.append("\t");
+ text.append("showUnconserved=");
+ text.append(sg.getShowNonconserved());
+ text.append("\t");
+ if (sg.textColour != java.awt.Color.black)
+ {
+ text.append("textCol1=");
+ text.append(jalview.util.Format.getHexString(sg.textColour));
+ text.append("\t");
+ }
+ if (sg.textColour2 != java.awt.Color.white)
+ {
+ text.append("textCol2=");
+ text.append(jalview.util.Format.getHexString(sg.textColour2));
+ text.append("\t");
+ }
+ if (sg.thresholdTextColour != 0)
+ {
+ text.append("textColThreshold=");
+ text.append(sg.thresholdTextColour);
+ text.append("\t");
+ }
+ if (sg.idColour != null)
+ {
+ text.append("idColour=");
+ text.append(jalview.util.Format.getHexString(sg.idColour));
+ text.append("\t");
+ }
+ if (sg.isHidereps())
+ {
+ text.append("hide=true\t");
+ }
+ if (sg.isHideCols())
+ {
+ text.append("hidecols=true\t");
+ }
+ if (seqrep != null)
+ {
+ // terminate the last line and clear the sequence ref for the group
+ text.append(newline);
+ text.append("SEQUENCE_REF");
+ }
+ text.append(newline);
+ text.append(newline);
+
+ }
+ }
+
+ SequenceI refSeq = null;
+
+ String refSeqId = null;
+
+ public boolean readAnnotationFile(AlignmentI al, String file,
+ String protocol)
+ {
+ BufferedReader in = null;
+ try
+ {
+ if (protocol.equals(AppletFormatAdapter.FILE))
+ {
+ in = new BufferedReader(new FileReader(file));
+ }
+ else if (protocol.equals(AppletFormatAdapter.URL))
+ {
+ URL url = new URL(file);
+ in = new BufferedReader(new InputStreamReader(url.openStream()));
+ }
+ else if (protocol.equals(AppletFormatAdapter.PASTE))
+ {
+ in = new BufferedReader(new StringReader(file));
+ }
+ else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))
+ {
+ java.io.InputStream is = getClass().getResourceAsStream("/" + file);
+ if (is != null)
+ {
+ in = new BufferedReader(new java.io.InputStreamReader(is));
+ }
+ }
+ if (in != null)
+ {
+ return parseAnnotationFrom(al, in);
+ }
+
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ System.out.println("Problem reading annotation file: " + ex);
+ if (nlinesread > 0)
+ {
+ System.out.println("Last read line " + nlinesread + ": '"
+ + lastread + "' (first 80 chars) ...");
+ }
+ return false;
+ }
+ return false;
+ }
+
+ long nlinesread = 0;
+
+ String lastread = "";
+
+ private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE";
+
+ public boolean parseAnnotationFrom(AlignmentI al, BufferedReader in)
+ throws Exception
+ {
+ nlinesread = 0;
+ ArrayList<Object[]> combineAnnotation_calls = new ArrayList<Object[]>();
+ ArrayList<Object[]> deferredAnnotation_calls = new ArrayList<Object[]>();
+ boolean modified = false;
+ String groupRef = null;
+ Hashtable groupRefRows = new Hashtable();
+
+ Hashtable autoAnnots = new Hashtable();
+ {
+ String line, label, description, token;
+ int graphStyle, index;
+ int refSeqIndex = 1;
+ int existingAnnotations = 0;
+ // when true - will add new rows regardless of whether they are duplicate
+ // auto-annotation like consensus or conservation graphs
+ boolean overrideAutoAnnot = false;
+ if (al.getAlignmentAnnotation() != null)
+ {
+ existingAnnotations = al.getAlignmentAnnotation().length;
+ if (existingAnnotations > 0)
+ {
+ AlignmentAnnotation[] aa = al.getAlignmentAnnotation();
+ for (int aai = 0; aai < aa.length; aai++)
+ {
+ if (aa[aai].autoCalculated)
+ {
+ // make a note of the name and description
+ autoAnnots.put(
+ autoAnnotsKey(aa[aai], aa[aai].sequenceRef,
+ (aa[aai].groupRef == null ? null
+ : aa[aai].groupRef.getName())),
+ new Integer(1));
+ }
+ }
+ }
+ }
+
+ int alWidth = al.getWidth();
+
+ StringTokenizer st;
+ Annotation[] annotations;
+ AlignmentAnnotation annotation = null;
+
+ // First confirm this is an Annotation file
+ boolean jvAnnotationFile = false;
+ while ((line = in.readLine()) != null)
+ {
+ nlinesread++;
+ lastread = new String(line);
+ if (line.indexOf("#") == 0)
+ {
+ continue;
+ }
+
+ if (line.indexOf("JALVIEW_ANNOTATION") > -1)
+ {
+ jvAnnotationFile = true;
+ break;
+ }
+ }
+
+ if (!jvAnnotationFile)
+ {
+ in.close();
+ return false;
+ }
+
+ while ((line = in.readLine()) != null)
+ {
+ nlinesread++;
+ lastread = new String(line);
+ if (line.indexOf("#") == 0
+ || line.indexOf("JALVIEW_ANNOTATION") > -1
+ || line.length() == 0)
+ {
+ continue;
+ }
+
+ st = new StringTokenizer(line, "\t");
+ token = st.nextToken();
+ if (token.equalsIgnoreCase("COLOUR"))
+ {
+ // TODO: use graduated colour def'n here too
+ colourAnnotations(al, st.nextToken(), st.nextToken());
+ modified = true;
+ continue;
+ }
+
+ else if (token.equalsIgnoreCase(COMBINE))
+ {
+ // keep a record of current state and resolve groupRef at end
+ combineAnnotation_calls.add(new Object[]
+ { st, refSeq, groupRef });
+ modified = true;
+ continue;
+ }
+ else if (token.equalsIgnoreCase("ROWPROPERTIES"))
+ {
+ addRowProperties(al, st);
+ modified = true;
+ continue;
+ }
+ else if (token.equalsIgnoreCase(GRAPHLINE))
+ {
+ // resolve at end
+ deferredAnnotation_calls.add(new Object[]
+ { GRAPHLINE, st, refSeq, groupRef });
+ modified = true;
+ continue;
+ }
+
+ else if (token.equalsIgnoreCase("SEQUENCE_REF"))
+ {
+ if (st.hasMoreTokens())
+ {
+ refSeq = al.findName(refSeqId = st.nextToken());
+ if (refSeq == null)
+ {
+ refSeqId = null;
+ }
+ try
+ {
+ refSeqIndex = Integer.parseInt(st.nextToken());
+ if (refSeqIndex < 1)
+ {
+ refSeqIndex = 1;
+ System.out
+ .println("WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile");
+ }
+ } catch (Exception ex)
+ {
+ refSeqIndex = 1;
+ }
+ }
+ else
+ {
+ refSeq = null;
+ refSeqId = null;
+ }
+ continue;
+ }
+ else if (token.equalsIgnoreCase("GROUP_REF"))
+ {
+ // Group references could be forward or backwards, so they are
+ // resolved after the whole file is read in
+ groupRef = null;
+ if (st.hasMoreTokens())
+ {
+ groupRef = st.nextToken();
+ if (groupRef.length() < 1)
+ {
+ groupRef = null; // empty string
+ }
+ else
+ {
+ if (groupRefRows.get(groupRef) == null)
+ {
+ groupRefRows.put(groupRef, new Vector());
+ }
+ }
+ }
+ continue;
+ }
+ else if (token.equalsIgnoreCase("SEQUENCE_GROUP"))
+ {
+ addGroup(al, st);
+ modified = true;
+ continue;
+ }
+
+ else if (token.equalsIgnoreCase("PROPERTIES"))
+ {
+ addProperties(al, st);
+ modified = true;
+ continue;
+ }
+
+ else if (token.equalsIgnoreCase("BELOW_ALIGNMENT"))
+ {
+ setBelowAlignment(al, st);
+ modified = true;
+ continue;
+ }
+ else if (token.equalsIgnoreCase("ALIGNMENT"))
+ {
+ addAlignmentDetails(al, st);
+ modified = true;
+ continue;
+ }
+
+ // Parse out the annotation row
+ graphStyle = AlignmentAnnotation.getGraphValueFromString(token);
+ label = st.nextToken();
+
+ index = 0;
+ annotations = new Annotation[alWidth];
+ description = null;
+ float score = Float.NaN;
+
+ if (st.hasMoreTokens())
+ {
+ line = st.nextToken();
+
+ if (line.indexOf("|") == -1)
+ {
+ description = line;
+ if (st.hasMoreTokens())
+ line = st.nextToken();
+ }
+
+ if (st.hasMoreTokens())
+ {
+ // This must be the score
+ score = Float.valueOf(st.nextToken()).floatValue();
+ }
+
+ st = new StringTokenizer(line, "|", true);
+
+ boolean emptyColumn = true;
+ boolean onlyOneElement = (st.countTokens() == 1);
+
+ while (st.hasMoreElements() && index < alWidth)
+ {
+ token = st.nextToken().trim();
+
+ if (onlyOneElement)
+ {
+ try
+ {
+ score = Float.valueOf(token).floatValue();
+ break;
+ } catch (NumberFormatException ex)
+ {
+ }
+ }
+
+ if (token.equals("|"))
+ {
+ if (emptyColumn)
+ {
+ index++;
+ }
+
+ emptyColumn = true;
+ }
+ else
+ {
+ annotations[index++] = parseAnnotation(token, graphStyle);
+ emptyColumn = false;
+ }
+ }
+
+ }
+
+ annotation = new AlignmentAnnotation(label, description,
+ (index == 0) ? null : annotations, 0, 0, graphStyle);
+
+ annotation.score = score;
+ if (!overrideAutoAnnot
+ && autoAnnots.containsKey(autoAnnotsKey(annotation, refSeq,
+ groupRef)))
+ {
+ // skip - we've already got an automatic annotation of this type.
+ continue;
+ }
+ // otherwise add it!
+ if (refSeq != null)
+ {
+
+ annotation.belowAlignment = false;
+ // make a copy of refSeq so we can find other matches in the alignment
+ SequenceI referedSeq = refSeq;
+ do
+ {
+ // copy before we do any mapping business.
+ // TODO: verify that undo/redo with 1:many sequence associated
+ // annotations can be undone correctly
+ AlignmentAnnotation ann = new AlignmentAnnotation(annotation);
+ annotation
+ .createSequenceMapping(referedSeq, refSeqIndex, false);
+ annotation.adjustForAlignment();
+ referedSeq.addAlignmentAnnotation(annotation);
+ al.addAnnotation(annotation);
+ al.setAnnotationIndex(annotation,
+ al.getAlignmentAnnotation().length
+ - existingAnnotations - 1);
+ if (groupRef != null)
+ {
+ ((Vector) groupRefRows.get(groupRef)).addElement(annotation);
+ }
+ // and recover our virgin copy to use again if necessary.
+ annotation = ann;
+
+ } while (refSeqId != null
+ && (referedSeq = al.findName(referedSeq, refSeqId, true)) != null);
+ }
+ else
+ {
+ al.addAnnotation(annotation);
+ al.setAnnotationIndex(annotation,
+ al.getAlignmentAnnotation().length - existingAnnotations
+ - 1);
+ if (groupRef != null)
+ {
+ ((Vector) groupRefRows.get(groupRef)).addElement(annotation);
+ }
+ }
+ // and set modification flag
+ modified = true;
+ }
+ // Resolve the groupRefs
+ Hashtable<String, SequenceGroup> groupRefLookup = new Hashtable<String, SequenceGroup>();
+ Enumeration en = groupRefRows.keys();
+
+ while (en.hasMoreElements())
+ {
+ groupRef = (String) en.nextElement();
+ boolean matched = false;
+ // Resolve group: TODO: add a getGroupByName method to alignments
+ for (SequenceGroup theGroup : al.getGroups())
+ {
+ if (theGroup.getName().equals(groupRef))
+ {
+ if (matched)
+ {
+ // TODO: specify and implement duplication of alignment annotation
+ // for multiple group references.
+ System.err
+ .println("Ignoring 1:many group reference mappings for group name '"
+ + groupRef + "'");
+ }
+ else
+ {
+ matched = true;
+ Vector rowset = (Vector) groupRefRows.get(groupRef);
+ groupRefLookup.put(groupRef, theGroup);
+ if (rowset != null && rowset.size() > 0)
+ {
+ AlignmentAnnotation alan = null;
+ for (int elm = 0, elmSize = rowset.size(); elm < elmSize; elm++)
+ {
+ alan = (AlignmentAnnotation) rowset.elementAt(elm);
+ alan.groupRef = theGroup;
+ }
+ }
+ }
+ }
+ }
+ ((Vector) groupRefRows.get(groupRef)).removeAllElements();
+ }
+ // process any deferred attribute settings for each context
+ for (Object[] _deferred_args : deferredAnnotation_calls)
+ {
+ if (_deferred_args[0] == GRAPHLINE)
+ {
+ addLine(al,
+ (StringTokenizer) _deferred_args[1], // st
+ (SequenceI) _deferred_args[2], // refSeq
+ (_deferred_args[3] == null) ? null : groupRefLookup
+ .get((String) _deferred_args[3]) // the reference
+ // group, or null
+ );
+ }
+ }
+
+ // finally, combine all the annotation rows within each context.
+ /**
+ * number of combine statements in this annotation file. Used to create
+ * new groups for combined annotation graphs without disturbing existing
+ * ones
+ */
+ int combinecount = 0;
+ for (Object[] _combine_args : combineAnnotation_calls)
+ {
+ combineAnnotations(al,
+ ++combinecount,
+ (StringTokenizer) _combine_args[0], // st
+ (SequenceI) _combine_args[1], // refSeq
+ (_combine_args[2] == null) ? null : groupRefLookup
+ .get((String) _combine_args[2]) // the reference group,
+ // or null
+ );
+ }
+ }
+ return modified;
+ }
+
+ private Object autoAnnotsKey(AlignmentAnnotation annotation,
+ SequenceI refSeq, String groupRef)
+ {
+ return annotation.graph + "\t" + annotation.label + "\t"
+ + annotation.description + "\t"
+ + (refSeq != null ? refSeq.getDisplayId(true) : "");
+ }
+
+ Annotation parseAnnotation(String string, int graphStyle)
+ {
+ boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH); // don't
+ // do the
+ // glyph
+ // test
+ // if we
+ // don't
+ // want
+ // secondary
+ // structure
+ String desc = null, displayChar = null;
+ char ss = ' '; // secondaryStructure
+ float value = 0;
+ boolean parsedValue = false, dcset = false;
+
+ // find colour here
+ java.awt.Color colour = null;
+ int i = string.indexOf("[");
+ int j = string.indexOf("]");
+ if (i > -1 && j > -1)
+ {
+ UserColourScheme ucs = new UserColourScheme();
+
+ colour = ucs.getColourFromString(string.substring(i + 1, j));
+ if (i > 0 && string.charAt(i - 1) == ',')
+ {
+ // clip the preceding comma as well
+ i--;
+ }
+ string = string.substring(0, i) + string.substring(j + 1);
+ }
+
+ StringTokenizer st = new StringTokenizer(string, ",", true);
+ String token;
+ boolean seenContent = false;
+ int pass = 0;
+ while (st.hasMoreTokens())
+ {
+ pass++;
+ token = st.nextToken().trim();
+ if (token.equals(","))
+ {
+ if (!seenContent && parsedValue && !dcset)
+ {
+ // allow the value below the bar/line to be empty
+ dcset = true;
+ displayChar = " ";
+ }
+ seenContent = false;
+ continue;
+ }
+ else
+ {
+ seenContent = true;
+ }
+
+ if (!parsedValue)
+ {
+ try
+ {
+ displayChar = token;
+ // foo
+ value = new Float(token).floatValue();
+ parsedValue = true;
+ continue;
+ } catch (NumberFormatException ex)
+ {
+ }
+ }
+ else
+ {
+ if (token.length() == 1)
+ {
+ displayChar = token;
+ }
+ }
+ if (hasSymbols
+ && (token.equals("H") || token.equals("E")
+ || token.equals("S") || token.equals(" ")))
+ {
+ // Either this character represents a helix or sheet
+ // or an integer which can be displayed
+ ss = token.charAt(0);
+ if (displayChar.equals(token.substring(0, 1)))
+ {
+ displayChar = "";
+ }
+ }
+ else if (desc == null || (parsedValue && pass > 2))
+ {
+ desc = token;
+ }
+
+ }
+ // if (!dcset && string.charAt(string.length() - 1) == ',')
+ // {
+ // displayChar = " "; // empty display char symbol.
+ // }
+ if (displayChar != null && desc != null && desc.length() == 1)
+ {
+ if (displayChar.length() > 1)
+ {
+ // switch desc and displayChar - legacy support
+ String tmp = displayChar;
+ displayChar = desc;
+ desc = tmp;
+ }
+ else
+ {
+ if (displayChar.equals(desc))
+ {
+ // duplicate label - hangover from the 'robust parser' above
+ desc = null;
+ }
+ }
+ }
+ Annotation anot = new Annotation(displayChar, desc, ss, value);
+
+ anot.colour = colour;
+
+ return anot;
+ }
+
+ void colourAnnotations(AlignmentI al, String label, String colour)
+ {
+ UserColourScheme ucs = new UserColourScheme(colour);
+ Annotation[] annotations;
+ for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
+ {
+ if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(label))
+ {
+ annotations = al.getAlignmentAnnotation()[i].annotations;
+ for (int j = 0; j < annotations.length; j++)
+ {
+ if (annotations[j] != null)
+ {
+ annotations[j].colour = ucs.findColour('A');
+ }
+ }
+ }
+ }
+ }
+
+ void combineAnnotations(AlignmentI al, int combineCount,
+ StringTokenizer st, SequenceI seqRef, SequenceGroup groupRef)
+ {
+ String group = st.nextToken();
+ // First make sure we are not overwriting the graphIndex
+ int graphGroup = 0;
+ if (al.getAlignmentAnnotation() != null)
+ {
+ for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
+ {
+ AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
+
+ if (aa.graphGroup > graphGroup)
+ {
+ // try to number graphGroups in order of occurence.
+ graphGroup = aa.graphGroup + 1;
+ }
+ if (aa.sequenceRef == seqRef && aa.groupRef == groupRef
+ && aa.label.equalsIgnoreCase(group))
+ {
+ if (aa.graphGroup > -1)
+ {
+ graphGroup = aa.graphGroup;
+ }
+ else
+ {
+ if (graphGroup <= combineCount)
+ {
+ graphGroup = combineCount + 1;
+ }
+ aa.graphGroup = graphGroup;
+ }
+ break;
+ }
+ }
+
+ // Now update groups
+ while (st.hasMoreTokens())
+ {
+ group = st.nextToken();
+ for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
+ {
+ AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
+ if (aa.sequenceRef == seqRef && aa.groupRef == groupRef
+ && aa.label.equalsIgnoreCase(group))
+ {
+ aa.graphGroup = graphGroup;
+ break;
+ }
+ }
+ }
+ }
+ else
+ {
+ System.err
+ .println("Couldn't combine annotations. None are added to alignment yet!");
+ }
+ }
+
+ void addLine(AlignmentI al, StringTokenizer st, SequenceI seqRef,
+ SequenceGroup groupRef)
+ {
+ String group = st.nextToken();
+ AlignmentAnnotation annotation = null, alannot[] = al
+ .getAlignmentAnnotation();
+ float value = new Float(st.nextToken()).floatValue();
+ String label = st.hasMoreTokens() ? st.nextToken() : null;
+ java.awt.Color colour = null;
+ if (st.hasMoreTokens())
+ {
+ UserColourScheme ucs = new UserColourScheme(st.nextToken());
+ colour = ucs.findColour('A');
+ }
+ if (alannot != null)
+ {
+ for (int i = 0; i < alannot.length; i++)
+ {
+ if (alannot[i].label.equalsIgnoreCase(group)
+ && (seqRef == null || alannot[i].sequenceRef == seqRef)
+ && (groupRef == null || alannot[i].groupRef == groupRef))
+ {
+ alannot[i].setThreshold(new GraphLine(value, label, colour));
+ }
+ }
+ }
+ if (annotation == null)
+ {
+ return;
+ }
+ }
+
+ void addGroup(AlignmentI al, StringTokenizer st)
+ {
+ SequenceGroup sg = new SequenceGroup();
+ sg.setName(st.nextToken());
+ String rng = "";
+ try
+ {
+ rng = st.nextToken();
+ if (rng.length() > 0 && !rng.startsWith("*"))
+ {
+ sg.setStartRes(Integer.parseInt(rng) - 1);
+ }
+ else
+ {
+ sg.setStartRes(0);
+ }
+ rng = st.nextToken();
+ if (rng.length() > 0 && !rng.startsWith("*"))
+ {
+ sg.setEndRes(Integer.parseInt(rng) - 1);
+ }
+ else
+ {
+ sg.setEndRes(al.getWidth() - 1);
+ }
+ } catch (Exception e)
+ {
+ System.err
+ .println("Couldn't parse Group Start or End Field as '*' or a valid column or sequence index: '"
+ + rng + "' - assuming alignment width for group.");
+ // assume group is full width
+ sg.setStartRes(0);
+ sg.setEndRes(al.getWidth() - 1);
+ }
+
+ String index = st.nextToken();
+ if (index.equals("-1"))
+ {
+ while (st.hasMoreElements())
+ {
+ sg.addSequence(al.findName(st.nextToken()), false);
+ }
+ }
+ else
+ {
+ StringTokenizer st2 = new StringTokenizer(index, ",");
+
+ while (st2.hasMoreTokens())
+ {
+ String tmp = st2.nextToken();
+ if (tmp.equals("*"))
+ {
+ for (int i = 0; i < al.getHeight(); i++)
+ {
+ sg.addSequence(al.getSequenceAt(i), false);
+ }
+ }
+ else if (tmp.indexOf("-") >= 0)
+ {
+ StringTokenizer st3 = new StringTokenizer(tmp, "-");
+
+ int start = (Integer.parseInt(st3.nextToken()));
+ int end = (Integer.parseInt(st3.nextToken()));
+
+ if (end > start)
+ {
+ for (int i = start; i <= end; i++)
+ {
+ sg.addSequence(al.getSequenceAt(i - 1), false);
+ }
+ }
+ }
+ else
+ {
+ sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1), false);
+ }
+ }
+ }
+
+ if (refSeq != null)
+ {
+ sg.setStartRes(refSeq.findIndex(sg.getStartRes() + 1) - 1);
+ sg.setEndRes(refSeq.findIndex(sg.getEndRes() + 1) - 1);
+ sg.setSeqrep(refSeq);
+ }
+
+ if (sg.getSize() > 0)
+ {
+ al.addGroup(sg);
+ }
+ }
+
+ void addRowProperties(AlignmentI al, StringTokenizer st)
+ {
+ String label = st.nextToken(), keyValue, key, value;
+ boolean scaletofit = false, centerlab = false, showalllabs = false;
+ while (st.hasMoreTokens())
+ {
+ keyValue = st.nextToken();
+ key = keyValue.substring(0, keyValue.indexOf("="));
+ value = keyValue.substring(keyValue.indexOf("=") + 1);
+ if (key.equalsIgnoreCase("scaletofit"))
+ {
+ scaletofit = Boolean.valueOf(value).booleanValue();
+ }
+ if (key.equalsIgnoreCase("showalllabs"))
+ {
+ showalllabs = Boolean.valueOf(value).booleanValue();
+ }
+ if (key.equalsIgnoreCase("centrelabs"))
+ {
+ centerlab = Boolean.valueOf(value).booleanValue();
+ }
+ AlignmentAnnotation[] alr = al.getAlignmentAnnotation();
+ if (alr != null)
+ {
+ for (int i = 0; i < alr.length; i++)
+ {
+ if (alr[i].label.equalsIgnoreCase(label))
+ {
+ alr[i].centreColLabels = centerlab;
+ alr[i].scaleColLabel = scaletofit;
+ alr[i].showAllColLabels = showalllabs;
+ }
+ }
+ }
+ }
+ }
+
+ void addProperties(AlignmentI al, StringTokenizer st)
+ {
+
+ // So far we have only added groups to the annotationHash,
+ // the idea is in the future properties can be added to
+ // alignments, other annotations etc
+ if (al.getGroups() == null)
+ {
+ return;
+ }
+
+ String name = st.nextToken();
+ SequenceGroup sg = null;
+ for (SequenceGroup _sg : al.getGroups())
+ {
+ if ((sg = _sg).getName().equals(name))
+ {
+ break;
+ }
+ else
+ {
+ sg = null;
+ }
+ }
+
+ if (sg != null)
+ {
+ String keyValue, key, value;
+ ColourSchemeI def = sg.cs;
+ sg.cs = null;
+ while (st.hasMoreTokens())
+ {
+ keyValue = st.nextToken();
+ key = keyValue.substring(0, keyValue.indexOf("="));
+ value = keyValue.substring(keyValue.indexOf("=") + 1);
+
+ if (key.equalsIgnoreCase("description"))
+ {
+ sg.setDescription(value);
+ }
+ else if (key.equalsIgnoreCase("colour"))
+ {
+ sg.cs = ColourSchemeProperty.getColour(al, value);
+ }
+ else if (key.equalsIgnoreCase("pidThreshold"))
+ {
+ sg.cs.setThreshold(Integer.parseInt(value), true);
+
+ }
+ else if (key.equalsIgnoreCase("consThreshold"))
+ {
+ sg.cs.setConservationInc(Integer.parseInt(value));
+ Conservation c = new Conservation("Group",
+ ResidueProperties.propHash, 3, sg.getSequences(null),
+ sg.getStartRes(), sg.getEndRes() + 1);
+
+ c.calculate();
+ c.verdict(false, 25); // TODO: refer to conservation percent threshold
+
+ sg.cs.setConservation(c);
+
+ }
+ else if (key.equalsIgnoreCase("outlineColour"))
+ {
+ sg.setOutlineColour(new UserColourScheme(value).findColour('A'));
+ }
+ else if (key.equalsIgnoreCase("displayBoxes"))
+ {
+ sg.setDisplayBoxes(Boolean.valueOf(value).booleanValue());
+ }
+ else if (key.equalsIgnoreCase("showUnconserved"))
+ {
+ sg.setShowNonconserved(Boolean.valueOf(value).booleanValue());
+ }
+ else if (key.equalsIgnoreCase("displayText"))
+ {
+ sg.setDisplayText(Boolean.valueOf(value).booleanValue());
+ }
+ else if (key.equalsIgnoreCase("colourText"))
+ {
+ sg.setColourText(Boolean.valueOf(value).booleanValue());
+ }
+ else if (key.equalsIgnoreCase("textCol1"))
+ {
+ sg.textColour = new UserColourScheme(value).findColour('A');
+ }
+ else if (key.equalsIgnoreCase("textCol2"))
+ {
+ sg.textColour2 = new UserColourScheme(value).findColour('A');
+ }
+ else if (key.equalsIgnoreCase("textColThreshold"))
+ {
+ sg.thresholdTextColour = Integer.parseInt(value);
+ }
+ else if (key.equalsIgnoreCase("idColour"))
+ {
+ // consider warning if colour doesn't resolve to a real colour
+ sg.setIdColour((def = new UserColourScheme(value))
+ .findColour('A'));
+ }
+ else if (key.equalsIgnoreCase("hide"))
+ {
+ // see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=25847
+ sg.setHidereps(true);
+ }
+ else if (key.equalsIgnoreCase("hidecols"))
+ {
+ // see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=25847
+ sg.setHideCols(true);
+ }
+ sg.recalcConservation();
+ }
+ if (sg.cs == null)
+ {
+ sg.cs = def;
+ }
+ }
+ }
+
+ void setBelowAlignment(AlignmentI al, StringTokenizer st)
+ {
+ String token;
+ AlignmentAnnotation aa, ala[] = al.getAlignmentAnnotation();
+ if (ala == null)
+ {
+ System.err
+ .print("Warning - no annotation to set below for sequence associated annotation:");
+ }
+ while (st.hasMoreTokens())
+ {
+ token = st.nextToken();
+ if (ala == null)
+ {
+ System.err.print(" " + token);
+ }
+ else
+ {
+ for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
+ {
+ aa = al.getAlignmentAnnotation()[i];
+ if (aa.sequenceRef == refSeq && aa.label.equals(token))
+ {
+ aa.belowAlignment = true;
+ }
+ }
+ }
+ }
+ if (ala == null)
+ {
+ System.err.print("\n");
+ }
+ }
+
+ void addAlignmentDetails(AlignmentI al, StringTokenizer st)
+ {
+ String keyValue, key, value;
+ while (st.hasMoreTokens())
+ {
+ keyValue = st.nextToken();
+ key = keyValue.substring(0, keyValue.indexOf("="));
+ value = keyValue.substring(keyValue.indexOf("=") + 1);
+ al.setProperty(key, value);
+ }
+ }
+
+ /**
+ * Write annotations as a CSV file of the form 'label, value, value, ...' for
+ * each row.
+ *
+ * @param annotations
+ * @return CSV file as a string.
+ */
+ public String printCSVAnnotations(AlignmentAnnotation[] annotations)
+ {
+ StringBuffer sp = new StringBuffer();
+ for (int i = 0; i < annotations.length; i++)
+ {
+ String atos = annotations[i].toString();
+ int p = 0;
+ do
+ {
+ int cp = atos.indexOf("\n", p);
+ sp.append(annotations[i].label);
+ sp.append(",");
+ if (cp > p)
+ {
+ sp.append(atos.substring(p, cp + 1));
+ }
+ else
+ {
+ sp.append(atos.substring(p));
+ sp.append(newline);
+ }
+ p = cp + 1;
+ } while (p > 0);
+ }
+ return sp.toString();
+ }
+}
git://source.jalview.org / jalview.git / blobdiff