import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.UserColourScheme;
import jalview.structure.StructureSelectionManager;
+import jalview.util.ColorUtils;
+import java.awt.Color;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
-import java.io.IOException;
import java.io.InputStreamReader;
import java.io.StringReader;
import java.net.URL;
public class AnnotationFile
{
+ StringBuffer text;
+
+ SequenceI refSeq = null;
+
+ String refSeqId = null;
+
+ String[] StructModelHeader = null;
+
+ long nlinesread = 0;
+
+ String lastread = "";
+
+ /**
+ * used for resolving absolute references to resources relative to
+ * annotationFile location
+ */
+ String baseUri = "";
+
+ private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE",
+ STRUCTMODEL = "STRUCTMODEL",
+ HEADER_STRUCT_MODEL = "HEADER_STRUCT_MODEL";
+
public AnnotationFile()
{
init();
return newline;
}
- StringBuffer text;
private void init()
{
if (sg.cs != null)
{
text.append("colour=");
- text.append(ColourSchemeProperty.getColourName(sg.cs));
+ text.append(sg.cs.toString());
text.append("\t");
if (sg.cs.getThreshold() != 0)
{
}
}
- SequenceI refSeq = null;
-
- String refSeqId = null;
public boolean annotateAlignmentView(AlignViewportI viewport,
- String file, String protocol)
+ String file, DataSourceType protocol)
{
ColumnSelection colSel = viewport.getColumnSelection();
if (colSel == null)
}
public boolean readAnnotationFile(AlignmentI al, String file,
- String protocol)
+ DataSourceType sourceType)
{
- return readAnnotationFile(al, null, file, protocol);
+ return readAnnotationFile(al, null, file, sourceType);
}
public boolean readAnnotationFile(AlignmentI al, ColumnSelection colSel,
- String file, String protocol)
+ String file, DataSourceType sourceType)
{
baseUri = "";
BufferedReader in = null;
try
{
- if (protocol.equals(AppletFormatAdapter.FILE))
+ if (sourceType == DataSourceType.FILE)
{
in = new BufferedReader(new FileReader(file));
baseUri = new File(file).getParent();
baseUri += "/";
}
}
- else if (protocol.equals(AppletFormatAdapter.URL))
+ else if (sourceType == DataSourceType.URL)
{
URL url = new URL(file);
in = new BufferedReader(new InputStreamReader(url.openStream()));
baseUri = baseUri.substring(0, baseUri.lastIndexOf("/")) + "/";
}
}
- else if (protocol.equals(AppletFormatAdapter.PASTE))
+ else if (sourceType == DataSourceType.PASTE)
{
in = new BufferedReader(new StringReader(file));
// TODO - support mimencoded PDBs for a paste.. ?
baseUri = "";
}
- else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))
+ else if (sourceType == DataSourceType.CLASSLOADER)
{
java.io.InputStream is = getClass().getResourceAsStream("/" + file);
if (is != null)
return false;
}
- long nlinesread = 0;
-
- String lastread = "";
-
- /**
- * used for resolving absolute references to resources relative to
- * annotationFile location
- */
- String baseUri = "";
-
- private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE",
- STRUCTMODEL = "STRUCTMODEL";
public boolean parseAnnotationFrom(AlignmentI al, ColumnSelection colSel,
BufferedReader in) throws Exception
modified = true;
continue;
}
- // else if (token.equalsIgnoreCase("VIEW_DEF"))
- // {
- // addOrSetView(al,st);
- // modified = true;
- // continue;
- // }
else if (token.equalsIgnoreCase("VIEW_SETREF"))
{
if (refSeq != null)
modified = true;
continue;
}
+ else if (token.equalsIgnoreCase(HEADER_STRUCT_MODEL))
+ {
+ int hSize = st.countTokens();
+ StructModelHeader = new String[hSize];
+ for (int x = 0; x < hSize; x++)
+ {
+ StructModelHeader[x] = st.nextToken();
+ }
+ continue;
+ }
else if (token.equalsIgnoreCase(STRUCTMODEL))
{
boolean failedtoadd = true;
- // expect
- // STRUCTMODEL <QUERYID> <TemplateID> <URL to model> <URL to
- // alignment>
+ // expects STRUCTMODEL <Query> <TemplateSeqId> <ModelFile>
+ // <FastaMappingFile>
+ String querySeqId = !st.hasMoreTokens() ? "" : st.nextToken();
+ SequenceI querySeq = al.findName(querySeqId);
if (st.hasMoreTokens()) {
refSeq = al.findName(refSeqId = st.nextToken());
if (refSeq == null)
}
else
{
- String tempId = st.nextToken();
- String urlToModel = st.nextToken();
- String urlToPairwise = st.hasMoreTokens() ? st.nextToken()
- : "";
- if (add_structmodel(al, refSeq, tempId, urlToModel,
- urlToPairwise))
+ int tSize = st.countTokens() + 2;
+ String[] rowData = new String[tSize];
+ rowData[0] = querySeqId;
+ rowData[1] = refSeqId;
+ for (int x = 2; x < tSize; x++)
+ {
+ rowData[x] = st.nextToken();
+ }
+ if (processStructModel(al, querySeq, refSeq,
+ StructModelHeader, rowData, baseUri))
{
failedtoadd = false;
}
if (failedtoadd)
{
System.err
- .println("Need <QueryId> <TemplateId> <URL to Model> [<URL to pairwise alignment>] as tab separated fields after "
+ .println("Need minimum of <Query> <TemplateSeqId> <ModelFile> <FastaMappingFile> as tab separated fields after"
+ STRUCTMODEL);
} else {
modified = true;
}
/**
- * resolve a structural model and generate and add an alignment sequence for
- * it
+ * Resolve structural model to a reference sequence and register it to
+ * StructureSelectionManager
*
- * @param refSeq2
- * @param tempId
- * @param urlToModel
- * @param urlToPairwise
+ * @param al
+ * @param querySequence
+ * @param templateSeq
+ * @param structModelHeader
+ * @param structModelData
* @return true if model and sequence was added
*/
- private boolean add_structmodel(AlignmentI al, SequenceI refSeq2, String tempId,
- String urlToModel, String urlToPairwise)
+ static boolean processStructModel(AlignmentI al, SequenceI querySequence,
+ SequenceI templateSeq,
+ String[] structModelHeader,
+ String[] structModelData, String baseUri)
{
- String warningMessage = null, modelPath = null, modelProt = null, aliPath = null, aliProt = null;
+ String warningMessage = null;
boolean added = false;
try {
- // locate tempId. if it exists, will need to merge, otherwise:
- SequenceI templateSeq = al.findName(tempId);
- // 1. load urlToModel
- modelPath = resolveAbsolute(urlToModel);
- modelProt = AppletFormatAdapter.checkProtocol(modelPath);
- // need to transfer to local temp file ?
- PDBEntry modelpe = new PDBEntry(tempId, null, Type.FILE, modelPath);
- PDBEntry templpe = new PDBEntry(tempId, null, Type.FILE, modelPath);
- refSeq2.addPDBId(modelpe);
- aliPath = resolveAbsolute(urlToPairwise);
- aliProt = AppletFormatAdapter.checkProtocol(aliPath);
- // 2. load urlToPairwise
- AlignmentI pwa = new AppletFormatAdapter().readFile(aliPath, aliProt,
- "FASTA");
- SequenceI qPw = null, tPw = null;
- if (pwa != null)
- {
- // resolve query/template sequences in provided alignment
- qPw = pwa.findName(refSeqId);
- tPw = pwa.findName(tempId);
- }
- if (false)
- // (qPw != null && tPw != null)
- {
- // not yet complete
- // refalQ vvva--addrvvvtttddd
- // refalT ---aaaa---sss---ddd
- // profalQ ---v-v-v-a.-.-a---dd--r--vvvtt--td--dd
- // profalT ---.-.-.-aa-a-a---..--.--sss..--.d--dd
- // Pragmatic solution here:
- // Map templpe onto refalT only where refalT and refalQ are both
- // non-gaps
-
- // columns for start..end in refSeq2
- int[] gapMap = refSeq2.gapMap();
- // insert gaps in tPw
- int curi = 0, width = refSeq2.getLength();
- // TBC
- }
- else
- {
- // assume 1:1 - so synthesise sequences to use to construct mapping
- StructureFile pdbf = StructureSelectionManager
- .getStructureSelectionManager().setMapping(false,
- new SequenceI[] { refSeq2.getDatasetSequence() },
- null, modelPath, modelProt);
- refSeq2.getDatasetSequence().addPDBId(modelpe);
- if (templateSeq == null && tPw != null)
- {
- tPw.createDatasetSequence();
- tPw.getDatasetSequence().addPDBId(templpe); // needs to set mapping based on model yet...
- al.addSequence(tPw);
- added = true;
- }
- }
- // 3. pad/insert gaps in urlToPairwise according to gaps already present in
- // refSeq2
- // 4. add padded tempId sequence to alignment
- // 4. associate urlToModel with refSeq2 based on position map provided by
- // urlToPairwise
- // 5. associate urlToModel with tempId based on position map provided by
- // urlToPairwise
- // start a thread to load urlToModel and process/annotate sequences.
- } catch (IOException x)
+ String structureModelFile = resolveAbsolutePath(structModelData[2],
+ baseUri);
+ String fastaMappingFile = resolveAbsolutePath(structModelData[3],
+ baseUri);
+ // System.out.println("Model File >> " + structureModelFile);
+ // System.out.println("Fasta File >> " + fastaMappingFile);
+ String modelName = StructureFile.safeName(structureModelFile);
+ PDBEntry phyre2PDBEntry = new PDBEntry(modelName, " ",
+ Type.PDB,
+ structureModelFile);
+ String phyre2ModelDesc = generatePhyre2InfoHTMLTable(
+ structModelHeader, structModelData);
+ phyre2PDBEntry.setProperty("PHYRE2_MODEL_INFO", phyre2ModelDesc);
+ templateSeq.getDatasetSequence().addPDBId(phyre2PDBEntry);
+ if (querySequence != null)
+ {
+ querySequence.getDatasetSequence().addPDBId(phyre2PDBEntry);
+ }
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager();
+ ssm.registerPhyre2Template(structureModelFile, fastaMappingFile);
+ added = true;
+
+ } catch (Exception x)
{
warningMessage = x.toString();
} finally {
{
System.err.println("Warnings whilst processing STRUCTMODEL: "+warningMessage);
}
- return added;
}
+ return added;
+ }
+
+ static String generatePhyre2InfoHTMLTable(String[] structModelHeader,
+ String[] structModelData)
+ {
+ StringBuilder phyre2InfoBuilder = new StringBuilder();
+ if (isGenerateStructInfoHtml(structModelHeader, structModelData))
+ {
+ phyre2InfoBuilder.append("<html><table border=\"1\" width=100%>")
+ .append("<tr><td colspan=\"2\"><strong>Phyre2 Template Info</strong></td></tr>");
+ for (int x = 4; x < structModelData.length; x++)
+ {
+ phyre2InfoBuilder.append("<tr><td>").append(structModelHeader[x])
+ .append("</td><td>").append(structModelData[x])
+ .append("</td></tr>");
+ }
+ phyre2InfoBuilder.append("</table></html>");
+ }
+ return phyre2InfoBuilder.toString();
}
- private String resolveAbsolute(String relURI)
+ static boolean isGenerateStructInfoHtml(String[] header, String[] data)
+ {
+ boolean generate = true;
+ if (header == null || data == null)
+ {
+ return false;
+ }
+ if (header.length < 3 || data.length < 3)
+ {
+ generate = false;
+ }
+ return generate;
+ }
+
+ static String resolveAbsolutePath(String relURI, String _baseUri)
{
if (relURI.indexOf(":/") > -1 || relURI.startsWith("/")
- || "".equals(baseUri) || relURI.startsWith(baseUri))
+ || "".equals(_baseUri) || relURI.startsWith(_baseUri))
{
return relURI;
}
- return baseUri + relURI;
+ return _baseUri + relURI;
}
private void parseHideCols(ColumnSelection colSel, String nextToken)
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
+ // don't do the glyph test if we don't want secondary structure
+ boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH);
String desc = null, displayChar = null;
char ss = ' '; // secondaryStructure
float value = 0;
boolean parsedValue = false, dcset = false;
// find colour here
- java.awt.Color colour = null;
+ 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));
+ colour = ColorUtils.parseColourString(string.substring(i + 1,
+ j));
if (i > 0 && string.charAt(i - 1) == ',')
{
// clip the preceding comma as well
void colourAnnotations(AlignmentI al, String label, String colour)
{
- UserColourScheme ucs = new UserColourScheme(colour);
+ Color awtColour = ColorUtils.parseColourString(colour);
Annotation[] annotations;
for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
{
{
if (annotations[j] != null)
{
- annotations[j].colour = ucs.findColour('A');
+ annotations[j].colour = awtColour;
}
}
}
SequenceGroup groupRef)
{
String group = st.nextToken();
- AlignmentAnnotation annotation = null, alannot[] = al
- .getAlignmentAnnotation();
- float value = new Float(st.nextToken()).floatValue();
+ AlignmentAnnotation[] alannot = al.getAlignmentAnnotation();
+ String nextToken = st.nextToken();
+ float value = 0f;
+ try
+ {
+ value = Float.valueOf(nextToken);
+ } catch (NumberFormatException e)
+ {
+ System.err.println("line " + nlinesread + ": Threshold '" + nextToken
+ + "' invalid, setting to zero");
+ }
String label = st.hasMoreTokens() ? st.nextToken() : null;
- java.awt.Color colour = null;
+ Color colour = null;
if (st.hasMoreTokens())
{
- UserColourScheme ucs = new UserColourScheme(st.nextToken());
- colour = ucs.findColour('A');
+ colour = ColorUtils.parseColourString(st.nextToken());
}
if (alannot != null)
{
}
}
}
- if (annotation == null)
- {
- return;
- }
}
void addGroup(AlignmentI al, StringTokenizer st)
if (sg != null)
{
String keyValue, key, value;
- ColourSchemeI def = sg.cs;
- sg.cs = null;
+ ColourSchemeI def = sg.getColourScheme();
while (st.hasMoreTokens())
{
keyValue = st.nextToken();
}
else if (key.equalsIgnoreCase("colour"))
{
- sg.cs = ColourSchemeProperty.getColour(al, value);
+ sg.cs.setColourScheme(ColourSchemeProperty
+ .getColourScheme(al, value));
}
else if (key.equalsIgnoreCase("pidThreshold"))
{
else if (key.equalsIgnoreCase("consThreshold"))
{
sg.cs.setConservationInc(Integer.parseInt(value));
- Conservation c = new Conservation("Group", 3,
- sg.getSequences(null), sg.getStartRes(),
- sg.getEndRes() + 1);
+ Conservation c = new Conservation("Group", sg.getSequences(null),
+ sg.getStartRes(), sg.getEndRes() + 1);
c.calculate();
c.verdict(false, 25); // TODO: refer to conservation percent threshold
}
else if (key.equalsIgnoreCase("outlineColour"))
{
- sg.setOutlineColour(new UserColourScheme(value).findColour('A'));
+ sg.setOutlineColour(ColorUtils.parseColourString(value));
}
else if (key.equalsIgnoreCase("displayBoxes"))
{
}
else if (key.equalsIgnoreCase("textCol1"))
{
- sg.textColour = new UserColourScheme(value).findColour('A');
+ sg.textColour = ColorUtils.parseColourString(value);
}
else if (key.equalsIgnoreCase("textCol2"))
{
- sg.textColour2 = new UserColourScheme(value).findColour('A');
+ sg.textColour2 = ColorUtils.parseColourString(value);
}
else if (key.equalsIgnoreCase("textColThreshold"))
{
}
else if (key.equalsIgnoreCase("idColour"))
{
- // consider warning if colour doesn't resolve to a real colour
- sg.setIdColour((def = new UserColourScheme(value))
- .findColour('A'));
+ Color idColour = ColorUtils.parseColourString(value);
+ sg.setIdColour(idColour == null ? Color.black : idColour);
}
else if (key.equalsIgnoreCase("hide"))
{
}
sg.recalcConservation();
}
- if (sg.cs == null)
+ if (sg.getColourScheme() == null)
{
- sg.cs = def;
+ sg.setColourScheme(def);
}
}
}
git://source.jalview.org / jalview.git / blobdiff