X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=a22b7a49963c1473cc6b7f1ccd7f8914ff476ab5;hb=b8cd52fe7bed59130e5b080acfd42c3ef2effdbb;hp=206d97151022e986886123c1b513ad1d087c4e51;hpb=6849cc1cb983a45b4b8fd840f5ffc7d31ca80f33;p=jalview.git diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java index 206d971..a22b7a4 100755 --- a/src/jalview/io/AnnotationFile.java +++ b/src/jalview/io/AnnotationFile.java @@ -26,6 +26,8 @@ import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.DynamicData; +import jalview.datamodel.DynamicData.DataType; import jalview.datamodel.GraphLine; import jalview.datamodel.HiddenSequences; import jalview.datamodel.PDBEntry; @@ -1293,9 +1295,9 @@ public class AnnotationFile PDBEntry phyre2PDBEntry = new PDBEntry(modelName, " ", Type.PDB, structureModelFile); - String phyre2ModelDesc = generatePhyre2InfoHTMLTable( + List phyreDD = generatePhyreDynamicDataList( structModelHeader, structModelData); - phyre2PDBEntry.setProperty("PHYRE2_MODEL_INFO", phyre2ModelDesc); + phyre2PDBEntry.setProperty("DYNAMIC_DATA_PHYRE2", phyreDD); templateSeq.getDatasetSequence().addPDBId(phyre2PDBEntry); if (querySequence != null) { @@ -1318,37 +1320,33 @@ public class AnnotationFile return added; } - static String generatePhyre2InfoHTMLTable(String[] structModelHeader, - String[] structModelData) + static List generatePhyreDynamicDataList( + String[] headerArray, + String[] dataArray) { - StringBuilder phyre2InfoBuilder = new StringBuilder(); - if (isGenerateStructInfoHtml(structModelHeader, structModelData)) + + if (headerArray == null || dataArray == null) { - phyre2InfoBuilder.append("") - .append(""); - for (int x = 4; x < structModelData.length; x++) - { - phyre2InfoBuilder.append(""); - } - phyre2InfoBuilder.append("
Phyre2 Template Info
").append(structModelHeader[x]) - .append("").append(structModelData[x]) - .append("
"); + throw new IllegalArgumentException( + "Header or data arrays must not be null"); } - return phyre2InfoBuilder.toString(); - } - static boolean isGenerateStructInfoHtml(String[] header, String[] data) - { - boolean generate = true; - if (header == null || data == null) + if (headerArray.length != dataArray.length) { - return false; + throw new IllegalArgumentException( + "Header and data arrays must be of same lenght"); } - if (header.length < 3 || data.length < 3) + List dynamicDataList = new ArrayList(); + int x = 0; + for (String data : dataArray) { - generate = false; + // first four column should be hidden; + boolean show = (x > 4); + dynamicDataList.add(new DynamicData(headerArray[x], data, DataType.S, + "PHYRE2", show)); + x++; } - return generate; + return dynamicDataList; } static String resolveAbsolutePath(String relURI, String _baseUri)