X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=d85c3d894ca5775d0424799d8a29d3152a2efc2b;hb=481ae9f847bc4f1437b2cfbf6c61ed040bc61892;hp=d41cdd4122d6535b0ef4335aa56a9b17a6c0f668;hpb=9d2408483e451285fd555c3cd6e0273977acbaa7;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index d41cdd4..d85c3d8 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -20,12 +20,6 @@ */ package jalview.datamodel; -import java.util.Locale; - -import jalview.analysis.Rna; -import jalview.analysis.SecStrConsensus.SimpleBP; -import jalview.analysis.WUSSParseException; - import java.util.ArrayList; import java.util.Arrays; import java.util.Collection; @@ -33,9 +27,15 @@ import java.util.Collections; import java.util.HashMap; import java.util.Iterator; import java.util.List; +import java.util.Locale; import java.util.Map; import java.util.Map.Entry; +import jalview.analysis.Rna; +import jalview.analysis.SecStrConsensus.SimpleBP; +import jalview.analysis.WUSSParseException; +import jalview.structure.StructureImportSettings; + /** * DOCUMENT ME! * @@ -44,6 +44,7 @@ import java.util.Map.Entry; */ public class AlignmentAnnotation { + private static final String ANNOTATION_ID_PREFIX = "ann"; /* @@ -97,6 +98,21 @@ public class AlignmentAnnotation private long invalidrnastruc = -2; /** + * the type of temperature factor plot (if it is one) + */ + private StructureImportSettings.TFType tfType = StructureImportSettings.TFType.DEFAULT; + + public void setTFType(StructureImportSettings.TFType t) + { + tfType = t; + } + + public StructureImportSettings.TFType getTFType() + { + return tfType; + } + + /** * Updates the _rnasecstr field Determines the positions that base pair and * the positions of helices based on secondary structure from a Stockholm file * @@ -110,7 +126,7 @@ public class AlignmentAnnotation invalidrnastruc = -1; } catch (WUSSParseException px) { - // DEBUG System.out.println(px); + // DEBUG jalview.bin.Console.outPrintln(px); invalidrnastruc = px.getProblemPos(); } if (invalidrnastruc > -1) @@ -126,7 +142,8 @@ public class AlignmentAnnotation scaleColLabel = true; _markRnaHelices(); } - // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup()); + // jalview.bin.Console.outPrintln("featuregroup " + + // _rnasecstr[0].getFeatureGroup()); } @@ -140,10 +157,10 @@ public class AlignmentAnnotation { /* - * System.out.println(this.annotation._rnasecstr[x] + " Begin" + + * jalview.bin.Console.outPrintln(this.annotation._rnasecstr[x] + " Begin" + * this.annotation._rnasecstr[x].getBegin()); */ - // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup()); + // jalview.bin.Console.outPrintln(this.annotation._rnasecstr[x].getFeatureGroup()); int val = 0; try { @@ -183,7 +200,8 @@ public class AlignmentAnnotation return rnaSecondaryStructureEquivalent(that, true); } - public boolean rnaSecondaryStructureEquivalent(AlignmentAnnotation that, boolean compareType) + public boolean rnaSecondaryStructureEquivalent(AlignmentAnnotation that, + boolean compareType) { SequenceFeature[] thisSfArray = this.getRnaSecondaryStructure(); SequenceFeature[] thatSfArray = that.getRnaSecondaryStructure(); @@ -196,21 +214,28 @@ public class AlignmentAnnotation return false; } Arrays.sort(thisSfArray, new SFSortByEnd()); // probably already sorted - // like this + // like this Arrays.sort(thatSfArray, new SFSortByEnd()); // probably already sorted - // like this - for (int i=0; i < thisSfArray.length; i++) { + // like this + for (int i = 0; i < thisSfArray.length; i++) + { SequenceFeature thisSf = thisSfArray[i]; SequenceFeature thatSf = thatSfArray[i]; - if (compareType) { - if (thisSf.getType() == null || thatSf.getType() == null) { - if (thisSf.getType() == null && thatSf.getType() == null) { + if (compareType) + { + if (thisSf.getType() == null || thatSf.getType() == null) + { + if (thisSf.getType() == null && thatSf.getType() == null) + { continue; - } else { + } + else + { return false; } } - if (! thisSf.getType().equals(thatSf.getType())) { + if (!thisSf.getType().equals(thatSf.getType())) + { return false; } } @@ -282,6 +307,14 @@ public class AlignmentAnnotation public static final int LINE_GRAPH = 2; + public static final int CONTACT_MAP = 4; + + /** + * property that when set to non-empty string disables display of column + * groups defined on the contact matrix + */ + public static final String CONTACT_MAP_NOGROUPS = "CMNOGRPS"; + public boolean belowAlignment = true; public SequenceGroup groupRef = null; @@ -355,7 +388,7 @@ public class AlignmentAnnotation char firstChar = 0; for (int i = 0; i < annotations.length; i++) { - // DEBUG System.out.println(i + ": " + annotations[i]); + // DEBUG jalview.bin.Console.outPrintln(i + ": " + annotations[i]); if (annotations[i] == null) { continue; @@ -363,32 +396,35 @@ public class AlignmentAnnotation if (annotations[i].secondaryStructure == 'H' || annotations[i].secondaryStructure == 'E') { - // DEBUG System.out.println( "/H|E/ '" + + // DEBUG jalview.bin.Console.outPrintln( "/H|E/ '" + // annotations[i].secondaryStructure + "'"); hasIcons |= true; } else // Check for RNA secondary structure { - // DEBUG System.out.println( "/else/ '" + + // DEBUG jalview.bin.Console.outPrintln( "/else/ '" + // annotations[i].secondaryStructure + "'"); // TODO: 2.8.2 should this ss symbol validation check be a function in // RNA/ResidueProperties ? + // allow for DSSP extended code: + // https://www.wikidoc.org/index.php/Secondary_structure#The_DSSP_code + // GHITEBS as well as C and X (for missing?) if (annotations[i].secondaryStructure == '(' || annotations[i].secondaryStructure == '[' || annotations[i].secondaryStructure == '<' || annotations[i].secondaryStructure == '{' || annotations[i].secondaryStructure == 'A' - || annotations[i].secondaryStructure == 'B' - || annotations[i].secondaryStructure == 'C' + // || annotations[i].secondaryStructure == 'B' + // || annotations[i].secondaryStructure == 'C' || annotations[i].secondaryStructure == 'D' // || annotations[i].secondaryStructure == 'E' // ambiguous on // its own -- already checked above || annotations[i].secondaryStructure == 'F' - || annotations[i].secondaryStructure == 'G' + // || annotations[i].secondaryStructure == 'G' // || annotations[i].secondaryStructure == 'H' // ambiguous on // its own -- already checked above - || annotations[i].secondaryStructure == 'I' + // || annotations[i].secondaryStructure == 'I' || annotations[i].secondaryStructure == 'J' || annotations[i].secondaryStructure == 'K' || annotations[i].secondaryStructure == 'L' @@ -398,12 +434,12 @@ public class AlignmentAnnotation || annotations[i].secondaryStructure == 'P' || annotations[i].secondaryStructure == 'Q' || annotations[i].secondaryStructure == 'R' - || annotations[i].secondaryStructure == 'S' - || annotations[i].secondaryStructure == 'T' + // || annotations[i].secondaryStructure == 'S' + // || annotations[i].secondaryStructure == 'T' || annotations[i].secondaryStructure == 'U' || annotations[i].secondaryStructure == 'V' || annotations[i].secondaryStructure == 'W' - || annotations[i].secondaryStructure == 'X' + // || annotations[i].secondaryStructure == 'X' || annotations[i].secondaryStructure == 'Y' || annotations[i].secondaryStructure == 'Z') { @@ -412,7 +448,8 @@ public class AlignmentAnnotation } } - // System.out.println("displaychar " + annotations[i].displayCharacter); + // jalview.bin.Console.outPrintln("displaychar " + + // annotations[i].displayCharacter); if (annotations[i].displayCharacter == null || annotations[i].displayCharacter.length() == 0) @@ -797,6 +834,7 @@ public class AlignmentAnnotation { this.sequenceMapping = null; } + } // TODO: check if we need to do this: JAL-952 // if (this.isrna=annotation.isrna) @@ -1716,4 +1754,29 @@ public class AlignmentAnnotation return aa; } + /** + * convenience method to check for the 'CONTACT_MAP_NOGROUPS' property for + * this alignment annotation row + * + * @return true if no CONTACT_MAP_NOGROUPS property is found, or it is set to + * "" + */ + public boolean isShowGroupsForContactMatrix() + { + return getProperty(AlignmentAnnotation.CONTACT_MAP_NOGROUPS) == null + || "".equals( + getProperty(AlignmentAnnotation.CONTACT_MAP_NOGROUPS)); + } + + /** + * set the 'CONTACT_MAP_NOGROUPS' property for this alignment annotation row + * + * @see isShowGroupsForContactMatrix + */ + public void setShowGroupsForContactMatrix(boolean showGroups) + { + setProperty(AlignmentAnnotation.CONTACT_MAP_NOGROUPS, + showGroups ? "" : "nogroups"); + } + }