-Clazz.declarePackage ("jalview.datamodel");\r
-Clazz.load (null, "jalview.datamodel.AlignmentView", ["jalview.datamodel.Alignment", "$.CigarArray", "$.ColumnSelection", "$.SeqCigar", "$.SequenceGroup", "jalview.util.MessageManager", "$.ShiftList", "java.lang.Error", "java.util.ArrayList", "$.Vector"], function () {\r
-c$ = Clazz.decorateAsClass (function () {\r
-this.sequences = null;\r
-this.contigs = null;\r
-this.width = 0;\r
-this.firstCol = 0;\r
-this.scGroups = null;\r
-this.$isNa = false;\r
-if (!Clazz.isClassDefined ("jalview.datamodel.AlignmentView.ScGroup")) {\r
-jalview.datamodel.AlignmentView.$AlignmentView$ScGroup$ ();\r
-}\r
-this.selected = null;\r
-Clazz.instantialize (this, arguments);\r
-}, jalview.datamodel, "AlignmentView");\r
-Clazz.defineMethod (c$, "isNa", \r
-function () {\r
-return this.$isNa;\r
-});\r
-Clazz.makeConstructor (c$, \r
-function (alignment, columnSelection, selection, hasHiddenColumns, selectedRegionOnly, recordGroups) {\r
-this.construct ( new jalview.datamodel.CigarArray (alignment, (hasHiddenColumns ? columnSelection : null), (selectedRegionOnly ? selection : null)), (selectedRegionOnly && selection != null) ? selection.getStartRes () : 0);\r
-this.$isNa = alignment.isNucleotide ();\r
-var selseqs;\r
-if (selection != null && selection.getSize () > 0) {\r
-var sel = selection.getSequences (null);\r
-this.selected = new java.util.Vector ();\r
-selseqs = selection.getSequencesInOrder (alignment, selectedRegionOnly);\r
-} else {\r
-selseqs = alignment.getSequencesArray ();\r
-}var seqsets = new java.util.ArrayList ();\r
-var grps = new java.util.ArrayList ();\r
-var gg = alignment.getGroups ();\r
-grps.addAll (gg);\r
-var sgrps = null;\r
-var addedgps = null;\r
-if (grps != null) {\r
-if (selection != null && selectedRegionOnly) {\r
-var ssel = selection.getStartRes ();\r
-var esel = selection.getEndRes ();\r
-var isg = new java.util.ArrayList ();\r
-for (var sg, $sg = grps.iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {\r
-if (!(sg.getStartRes () > esel || sg.getEndRes () < ssel)) {\r
-if (sg.getStartRes () < ssel) {\r
-sg.setStartRes (ssel);\r
-}if (sg.getEndRes () > esel) {\r
-sg.setEndRes (esel);\r
-}sg.setStartRes (sg.getStartRes () - ssel + 1);\r
-sg.setEndRes (sg.getEndRes () - ssel + 1);\r
-isg.add (sg);\r
-}}\r
-grps = isg;\r
-}sgrps = new Array (grps.size ());\r
-addedgps = Clazz.newBooleanArray (grps.size (), false);\r
-for (var g = 0; g < sgrps.length; g++) {\r
-var sg = grps.get (g);\r
-sgrps[g] = Clazz.innerTypeInstance (jalview.datamodel.AlignmentView.ScGroup, this, null);\r
-sgrps[g].sg = new jalview.datamodel.SequenceGroup (sg);\r
-addedgps[g] = false;\r
-seqsets.add (sg.getSequences ());\r
-}\r
-}var csi = 0;\r
-for (var i = 0; i < selseqs.length; i++) {\r
-if (selseqs[i] != null) {\r
-if (selection != null && selection.getSize () > 0 && !selectedRegionOnly) {\r
-this.sequences[csi].setGroupMembership (this.selected);\r
-this.selected.addElement (this.sequences[csi]);\r
-}if (seqsets != null) {\r
-for (var sg = 0; sg < sgrps.length; sg++) {\r
-if ((seqsets.get (sg)).contains (selseqs[i])) {\r
-this.sequences[csi].setGroupMembership (sgrps[sg]);\r
-sgrps[sg].sg.deleteSequence (selseqs[i], false);\r
-sgrps[sg].seqs.addElement (this.sequences[csi]);\r
-if (!addedgps[sg]) {\r
-if (this.scGroups == null) {\r
-this.scGroups = new java.util.ArrayList ();\r
-}addedgps[sg] = true;\r
-this.scGroups.add (sgrps[sg]);\r
-}}}\r
-}csi++;\r
-}}\r
-for (var sg = 0; sg < sgrps.length; sg++) {\r
-var sqs = sgrps[sg].sg.getSequencesAsArray (null);\r
-for (var si = 0; si < sqs.length; si++) {\r
-sgrps[sg].sg.deleteSequence (sqs[si], false);\r
-}\r
-sgrps[sg] = null;\r
-}\r
-}, "jalview.datamodel.AlignmentI,jalview.datamodel.ColumnSelection,jalview.datamodel.SequenceGroup,~B,~B,~B");\r
-Clazz.makeConstructor (c$, \r
-function (seqcigararray) {\r
-if (!seqcigararray.isSeqCigarArray ()) {\r
-throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_can_only_make_alignmnet_from_cigararray"));\r
-}this.contigs = seqcigararray.getDeletedRegions ();\r
-this.sequences = seqcigararray.getSeqCigarArray ();\r
-this.width = seqcigararray.getWidth ();\r
-}, "jalview.datamodel.CigarArray");\r
-Clazz.makeConstructor (c$, \r
-function (sdata, firstcol) {\r
-this.construct (sdata);\r
-this.firstCol = firstcol;\r
-}, "jalview.datamodel.CigarArray,~N");\r
-Clazz.defineMethod (c$, "setSequences", \r
-function (sequences) {\r
-this.sequences = sequences;\r
-}, "~A");\r
-Clazz.defineMethod (c$, "setContigs", \r
-function (contigs) {\r
-this.contigs = contigs;\r
-}, "~A");\r
-Clazz.defineMethod (c$, "getSequences", \r
-function () {\r
-return this.sequences;\r
-});\r
-Clazz.defineMethod (c$, "getContigs", \r
-function () {\r
-return this.contigs;\r
-});\r
-Clazz.defineMethod (c$, "getAlignmentAndColumnSelection", \r
-function (gapCharacter) {\r
-var colsel = new jalview.datamodel.ColumnSelection ();\r
-return Clazz.newArray (-1, [jalview.datamodel.SeqCigar.createAlignmentSequences (this.sequences, gapCharacter, colsel, this.contigs), colsel]);\r
-}, "~S");\r
-Clazz.defineMethod (c$, "getVisibleAlignment", \r
-function (c) {\r
-var aln = this.getVisibleSeqs (c);\r
-var vcal = new jalview.datamodel.Alignment (aln);\r
-this.addPrunedGroupsInOrder (vcal, -1, -1, true);\r
-return vcal;\r
-}, "~S");\r
-Clazz.defineMethod (c$, "addPrunedGroupsInOrder", \r
-($fz = function (vcal, gstart, gend, viscontigs) {\r
-var r = false;\r
-if (gstart > -1 && gstart <= gend) {\r
-r = true;\r
-}var aln = vcal.getSequencesArray ();\r
-{\r
-{\r
-var nvg = (this.scGroups != null) ? this.scGroups.size () : 0;\r
-if (nvg > 0) {\r
-var nsg = new Array (nvg);\r
-for (var g = 0; g < nvg; g++) {\r
-var sg = this.scGroups.get (g).sg;\r
-if (r) {\r
-if (sg.getStartRes () > gend || sg.getEndRes () < gstart) {\r
-nsg[g] = null;\r
-continue;\r
-}}nsg[g] = new jalview.datamodel.SequenceGroup (sg);\r
-if (r && !viscontigs) {\r
-if (nsg[g].getStartRes () < gstart) {\r
-nsg[g].setStartRes (0);\r
-} else {\r
-nsg[g].setStartRes (nsg[g].getStartRes () - gstart);\r
-nsg[g].setEndRes (nsg[g].getEndRes () - gstart);\r
-}if (nsg[g].getEndRes () > (gend - gstart)) {\r
-nsg[g].setEndRes (gend - gstart);\r
-}}}\r
-if (viscontigs) {\r
-if (this.contigs != null) {\r
-var p = 0;\r
-var prune = new jalview.util.ShiftList ();\r
-if (r) {\r
-prune.addShift (gstart, -gstart);\r
-}for (var h = 0; h < this.contigs.length; h += 3) {\r
-{\r
-prune.addShift (p + this.contigs[h + 1], this.contigs[h + 2] - this.contigs[h + 1]);\r
-}p = this.contigs[h + 1] + this.contigs[h + 2];\r
-}\r
-for (var g = 0; g < nsg.length; g++) {\r
-if (nsg[g] != null) {\r
-var s = nsg[g].getStartRes ();\r
-var t = nsg[g].getEndRes ();\r
-var w = 1 + t - s;\r
-if (r) {\r
-if (s < gstart) {\r
-s = gstart;\r
-}if (t > gend) {\r
-t = gend;\r
-}}s = prune.shift (s);\r
-t = prune.shift (t);\r
-nsg[g].setStartRes (s);\r
-nsg[g].setEndRes (t);\r
-}}\r
-}}for (var nsq = 0; nsq < aln.length; nsq++) {\r
-for (var g = 0; g < nvg; g++) {\r
-if (nsg[g] != null && this.sequences[nsq].isMemberOf (this.scGroups.get (g))) {\r
-nsg[g].addSequence (aln[nsq], false);\r
-}}\r
-}\r
-for (var g = 0; g < nvg; g++) {\r
-if (nsg[g] != null && nsg[g].getSize () > 0) {\r
-vcal.addGroup (nsg[g]);\r
-}nsg[g] = null;\r
-}\r
-}}}}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentI,~N,~N,~B");\r
-Clazz.defineMethod (c$, "getVisibleSeqs", \r
-($fz = function (c) {\r
-var aln = new Array (this.sequences.length);\r
-for (var i = 0, j = this.sequences.length; i < j; i++) {\r
-aln[i] = this.sequences[i].getSeq ('-');\r
-}\r
-var seqs = this.getSequenceStrings ('-');\r
-for (var i = 0, j = aln.length; i < j; i++) {\r
-aln[i].setSequence (seqs[i]);\r
-}\r
-return aln;\r
-}, $fz.isPrivate = true, $fz), "~S");\r
-Clazz.defineMethod (c$, "getVisibleContigAlignments", \r
-function (c) {\r
-var nvc = 0;\r
-var vcontigs = this.getVisibleContigs ();\r
-var contigviews = this.getVisibleContigs (c);\r
-var vcals = new Array (contigviews.length);\r
-for (nvc = 0; nvc < contigviews.length; nvc++) {\r
-vcals[nvc] = new jalview.datamodel.Alignment (contigviews[nvc]);\r
-if (this.scGroups != null && this.scGroups.size () > 0) {\r
-this.addPrunedGroupsInOrder (vcals[nvc], vcontigs[nvc * 2], vcontigs[nvc * 2 + 1], true);\r
-}}\r
-return vcals;\r
-}, "~S");\r
-Clazz.defineMethod (c$, "getSequenceStrings", \r
-function (c) {\r
-var seqs = new Array (this.sequences.length);\r
-for (var n = 0; n < this.sequences.length; n++) {\r
-var fullseq = this.sequences[n].getSequenceString (c);\r
-if (this.contigs != null) {\r
-seqs[n] = "";\r
-var p = 0;\r
-for (var h = 0; h < this.contigs.length; h += 3) {\r
-seqs[n] += fullseq.substring (p, this.contigs[h + 1]);\r
-p = this.contigs[h + 1] + this.contigs[h + 2];\r
-}\r
-seqs[n] += fullseq.substring (p);\r
-} else {\r
-seqs[n] = fullseq;\r
-}}\r
-return seqs;\r
-}, "~S");\r
-Clazz.defineMethod (c$, "getWidth", \r
-function () {\r
-return this.width;\r
-});\r
-Clazz.defineMethod (c$, "setWidth", \r
-function (width) {\r
-this.width = width;\r
-}, "~N");\r
-Clazz.defineMethod (c$, "getVisibleContigs", \r
-function (gapCharacter) {\r
-var smsa;\r
-var njobs = 1;\r
-if (this.sequences == null || this.width <= 0) {\r
-return null;\r
-}if (this.contigs != null && this.contigs.length > 0) {\r
-var start = 0;\r
-njobs = 0;\r
-var fwidth = this.width;\r
-for (var contig = 0; contig < this.contigs.length; contig += 3) {\r
-if ((this.contigs[contig + 1] - start) > 0) {\r
-njobs++;\r
-}fwidth += this.contigs[contig + 2];\r
-start = this.contigs[contig + 1] + this.contigs[contig + 2];\r
-}\r
-if (start < fwidth) {\r
-njobs++;\r
-}smsa = new Array (njobs);\r
-start = 0;\r
-var j = 0;\r
-for (var contig = 0; contig < this.contigs.length; contig += 3) {\r
-if (this.contigs[contig + 1] - start > 0) {\r
-var mseq = new Array (this.sequences.length);\r
-for (var s = 0; s < mseq.length; s++) {\r
-mseq[s] = this.sequences[s].getSeq (gapCharacter).getSubSequence (start, this.contigs[contig + 1]);\r
-}\r
-smsa[j] = mseq;\r
-j++;\r
-}start = this.contigs[contig + 1] + this.contigs[contig + 2];\r
-}\r
-if (start < fwidth) {\r
-var mseq = new Array (this.sequences.length);\r
-for (var s = 0; s < mseq.length; s++) {\r
-mseq[s] = this.sequences[s].getSeq (gapCharacter).getSubSequence (start, fwidth + 1);\r
-}\r
-smsa[j] = mseq;\r
-j++;\r
-}} else {\r
-smsa = new Array (1);\r
-smsa[0] = new Array (this.sequences.length);\r
-for (var s = 0; s < this.sequences.length; s++) {\r
-smsa[0][s] = this.sequences[s].getSeq (gapCharacter);\r
-}\r
-}return smsa;\r
-}, "~S");\r
-Clazz.defineMethod (c$, "getUpdatedView", \r
-function (nvismsa, orders, gapCharacter) {\r
-if (this.sequences == null || this.width <= 0) {\r
-throw new Error (jalview.util.MessageManager.getString ("error.empty_view_cannot_be_updated"));\r
-}if (nvismsa == null) {\r
-throw new Error ("nvismsa==null. use getAlignmentAndColumnSelection() instead.");\r
-}if (this.contigs != null && this.contigs.length > 0) {\r
-var alignment = new Array (this.sequences.length);\r
-var columnselection = new jalview.datamodel.ColumnSelection ();\r
-if (this.contigs != null && this.contigs.length > 0) {\r
-var start = 0;\r
-var nwidth = 0;\r
-var owidth = this.width;\r
-var j = 0;\r
-for (var contig = 0; contig < this.contigs.length; contig += 3) {\r
-owidth += this.contigs[contig + 2];\r
-if (this.contigs[contig + 1] - start > 0) {\r
-var swidth = 0;\r
-if (nvismsa[j] != null) {\r
-var mseq = nvismsa[j];\r
-var order = (orders == null) ? null : orders[j];\r
-j++;\r
-if (mseq.length != this.sequences.length) {\r
-throw new Error (jalview.util.MessageManager.formatMessage ("error.mismatch_between_number_of_sequences_in_block", Clazz.newArray (-1, [Integer.$valueOf (j).toString (), Integer.$valueOf (mseq.length).toString (), Integer.$valueOf (this.sequences.length).toString ()])));\r
-}swidth = mseq[0].getLength ();\r
-for (var s = 0; s < mseq.length; s++) {\r
-if (alignment[s] == null) {\r
-alignment[s] = mseq[s];\r
-} else {\r
-alignment[s].setSequence (alignment[s].getSequenceAsString () + mseq[s].getSequenceAsString ());\r
-if (mseq[s].getStart () <= mseq[s].getEnd ()) {\r
-alignment[s].setEnd (mseq[s].getEnd ());\r
-}if (order != null) {\r
-order.updateSequence (mseq[s], alignment[s]);\r
-}}}\r
-} else {\r
-if (true) {\r
-for (var s = 0; s < this.sequences.length; s++) {\r
-var oseq = this.sequences[s].getSeq (gapCharacter).getSubSequence (start, this.contigs[contig + 1]);\r
-if (swidth < oseq.getLength ()) {\r
-swidth = oseq.getLength ();\r
-}if (alignment[s] == null) {\r
-alignment[s] = oseq;\r
-} else {\r
-alignment[s].setSequence (alignment[s].getSequenceAsString () + oseq.getSequenceAsString ());\r
-if (oseq.getEnd () >= oseq.getStart ()) {\r
-alignment[s].setEnd (oseq.getEnd ());\r
-}}}\r
-}j++;\r
-}nwidth += swidth;\r
-}start = this.contigs[contig + 1] + this.contigs[contig + 2];\r
-for (var s = 0; s < this.sequences.length; s++) {\r
-var hseq = this.sequences[s].getSeq (gapCharacter).getSubSequence (this.contigs[contig + 1], start);\r
-if (alignment[s] == null) {\r
-alignment[s] = hseq;\r
-} else {\r
-alignment[s].setSequence (alignment[s].getSequenceAsString () + hseq.getSequenceAsString ());\r
-if (hseq.getEnd () >= hseq.getStart ()) {\r
-alignment[s].setEnd (hseq.getEnd ());\r
-}}}\r
-columnselection.hideColumns (nwidth, nwidth + this.contigs[contig + 2] - 1);\r
-nwidth += this.contigs[contig + 2];\r
-}\r
-if (j < nvismsa.length) {\r
-var swidth = 0;\r
-if (nvismsa[j] != null) {\r
-var mseq = nvismsa[j];\r
-var order = (orders != null) ? orders[j] : null;\r
-swidth = mseq[0].getLength ();\r
-for (var s = 0; s < mseq.length; s++) {\r
-if (alignment[s] == null) {\r
-alignment[s] = mseq[s];\r
-} else {\r
-alignment[s].setSequence (alignment[s].getSequenceAsString () + mseq[s].getSequenceAsString ());\r
-if (mseq[s].getEnd () >= mseq[s].getStart ()) {\r
-alignment[s].setEnd (mseq[s].getEnd ());\r
-}if (order != null) {\r
-order.updateSequence (mseq[s], alignment[s]);\r
-}}}\r
-} else {\r
-if (start < owidth) {\r
-if (true) {\r
-for (var s = 0; s < this.sequences.length; s++) {\r
-var oseq = this.sequences[s].getSeq (gapCharacter).getSubSequence (start, owidth + 1);\r
-if (swidth < oseq.getLength ()) {\r
-swidth = oseq.getLength ();\r
-}if (alignment[s] == null) {\r
-alignment[s] = oseq;\r
-} else {\r
-alignment[s].setSequence (alignment[s].getSequenceAsString () + oseq.getSequenceAsString ());\r
-if (oseq.getEnd () >= oseq.getStart ()) {\r
-alignment[s].setEnd (oseq.getEnd ());\r
-}}}\r
-nwidth += swidth;\r
-} else {\r
-throw new Error (jalview.util.MessageManager.getString ("error.padding_not_yet_implemented"));\r
-}}}}}return Clazz.newArray (-1, [alignment, columnselection]);\r
-} else {\r
-if (nvismsa.length != 1) {\r
-throw new Error (jalview.util.MessageManager.formatMessage ("error.mismatch_between_visible_blocks_to_update_and_number_of_contigs_in_view", Clazz.newArray (-1, [Integer.$valueOf (nvismsa.length).toString ()])));\r
-}if (nvismsa[0] != null) {\r
-return Clazz.newArray (-1, [nvismsa[0], new jalview.datamodel.ColumnSelection ()]);\r
-} else {\r
-return this.getAlignmentAndColumnSelection (gapCharacter);\r
-}}}, "~A,~A,~S");\r
-Clazz.defineMethod (c$, "getVisibleContigs", \r
-function () {\r
-if (this.contigs != null && this.contigs.length > 0) {\r
-var start = 0;\r
-var nvis = 0;\r
-var fwidth = this.width;\r
-for (var contig = 0; contig < this.contigs.length; contig += 3) {\r
-if ((this.contigs[contig + 1] - start) > 0) {\r
-nvis++;\r
-}fwidth += this.contigs[contig + 2];\r
-start = this.contigs[contig + 1] + this.contigs[contig + 2];\r
-}\r
-if (start < fwidth) {\r
-nvis++;\r
-}var viscontigs = Clazz.newIntArray (nvis * 2, 0);\r
-nvis = 0;\r
-start = 0;\r
-for (var contig = 0; contig < this.contigs.length; contig += 3) {\r
-if ((this.contigs[contig + 1] - start) > 0) {\r
-viscontigs[nvis] = start;\r
-viscontigs[nvis + 1] = this.contigs[contig + 1] - 1;\r
-nvis += 2;\r
-}start = this.contigs[contig + 1] + this.contigs[contig + 2];\r
-}\r
-if (start < fwidth) {\r
-viscontigs[nvis] = start;\r
-viscontigs[nvis + 1] = fwidth;\r
-nvis += 2;\r
-}return viscontigs;\r
-} else {\r
-return Clazz.newIntArray (-1, [0, this.width]);\r
-}});\r
-Clazz.defineMethod (c$, "getAlignmentOrigin", \r
-function () {\r
-return this.firstCol;\r
-});\r
-Clazz.defineMethod (c$, "getVisibleContigMapFor", \r
-function (gapMap) {\r
-var delMap = null;\r
-var viscontigs = this.getVisibleContigs ();\r
-var spos = 0;\r
-var i = 0;\r
-if (viscontigs != null) {\r
-delMap = Clazz.newIntArray (gapMap.length, 0);\r
-for (var contig = 0; contig < viscontigs.length; contig += 2) {\r
-while (spos < gapMap.length && gapMap[spos] < viscontigs[contig]) {\r
-spos++;\r
-}\r
-while (spos < gapMap.length && gapMap[spos] <= viscontigs[contig + 1]) {\r
-delMap[i++] = spos++;\r
-}\r
-}\r
-var tmap = Clazz.newIntArray (i, 0);\r
-System.arraycopy (delMap, 0, tmap, 0, i);\r
-delMap = tmap;\r
-}return delMap;\r
-}, "~A");\r
-Clazz.defineMethod (c$, "getEditedSequences", \r
-function (gc, $delete) {\r
-var msf = this.getSequences ();\r
-var aln = new Array (msf.length);\r
-for (var i = 0, j = msf.length; i < j; i++) {\r
-aln[i] = msf[i].getSeq (gc);\r
-}\r
-if ($delete) {\r
-var sqs = this.getSequenceStrings (gc);\r
-for (var i = 0; i < sqs.length; i++) {\r
-aln[i].setSequence (sqs[i]);\r
-sqs[i] = null;\r
-}\r
-}return aln;\r
-}, "~S,~B");\r
-c$.summariseAlignmentView = Clazz.defineMethod (c$, "summariseAlignmentView", \r
-function (view, os) {\r
-os.print ("View has " + view.sequences.length + " of which ");\r
-if (view.selected == null) {\r
-os.print ("None");\r
-} else {\r
-os.print (" " + view.selected.size ());\r
-}os.println (" are selected.");\r
-os.print ("View is " + view.getWidth () + " columns wide");\r
-var viswid = 0;\r
-var contigs = view.getContigs ();\r
-if (contigs != null) {\r
-viswid = view.width;\r
-for (var i = 0; i < contigs.length; i += 3) {\r
-viswid += contigs[i + 2];\r
-}\r
-os.println ("with " + viswid + " visible columns spread over " + Clazz.doubleToInt (contigs.length / 3) + " regions.");\r
-} else {\r
-viswid = view.width;\r
-os.println (".");\r
-}if (view.scGroups != null) {\r
-os.println ("There are " + view.scGroups.size () + " groups defined on the view.");\r
-for (var g = 0; g < view.scGroups.size (); g++) {\r
-var sgr = view.scGroups.get (g);\r
-os.println ("Group " + g + ": Name = " + sgr.sg.getName () + " Contains " + sgr.seqs.size () + " Seqs.");\r
-os.println ("This group runs from " + sgr.sg.getStartRes () + " to " + sgr.sg.getEndRes ());\r
-for (var s = 0; s < sgr.seqs.size (); s++) {\r
-if (!(sgr.seqs.elementAt (s)).isMemberOf (sgr)) {\r
-os.println ("** WARNING: sequence " + (sgr.seqs.elementAt (s)).toString () + " is not marked as member of group.");\r
-}}\r
-}\r
-var visal = view.getVisibleAlignment ('-');\r
-if (visal != null) {\r
-os.println ("Vis. alignment is " + visal.getWidth () + " wide and has " + visal.getHeight () + " seqs.");\r
-if (visal.getGroups () != null && visal.getGroups ().size () > 0) {\r
-var i = 1;\r
-for (var sg, $sg = visal.getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {\r
-os.println ("Group " + (i++) + " begins at column " + sg.getStartRes () + " and ends at " + sg.getEndRes ());\r
-}\r
-}}}}, "jalview.datamodel.AlignmentView,java.io.PrintStream");\r
-c$.testSelectionViews = Clazz.defineMethod (c$, "testSelectionViews", \r
-function (alignment, csel, selection) {\r
-System.out.println ("Testing standard view creation:\n");\r
-var view = null;\r
-try {\r
-System.out.println ("View with no hidden columns, no limit to selection, no groups to be collected:");\r
-view = new jalview.datamodel.AlignmentView (alignment, csel, selection, false, false, false);\r
-jalview.datamodel.AlignmentView.summariseAlignmentView (view, System.out);\r
-} catch (e) {\r
-if (Clazz.exceptionOf (e, Exception)) {\r
-e.printStackTrace ();\r
-System.err.println ("Failed to generate alignment with selection but no groups marked.");\r
-} else {\r
-throw e;\r
-}\r
-}\r
-try {\r
-System.out.println ("View with no hidden columns, no limit to selection, and all groups to be collected:");\r
-view = new jalview.datamodel.AlignmentView (alignment, csel, selection, false, false, true);\r
-jalview.datamodel.AlignmentView.summariseAlignmentView (view, System.out);\r
-} catch (e) {\r
-if (Clazz.exceptionOf (e, Exception)) {\r
-e.printStackTrace ();\r
-System.err.println ("Failed to generate alignment with selection marked but no groups marked.");\r
-} else {\r
-throw e;\r
-}\r
-}\r
-try {\r
-System.out.println ("View with no hidden columns, limited to selection and no groups to be collected:");\r
-view = new jalview.datamodel.AlignmentView (alignment, csel, selection, false, true, false);\r
-jalview.datamodel.AlignmentView.summariseAlignmentView (view, System.out);\r
-} catch (e) {\r
-if (Clazz.exceptionOf (e, Exception)) {\r
-e.printStackTrace ();\r
-System.err.println ("Failed to generate alignment with selection restricted but no groups marked.");\r
-} else {\r
-throw e;\r
-}\r
-}\r
-try {\r
-System.out.println ("View with no hidden columns, limited to selection, and all groups to be collected:");\r
-view = new jalview.datamodel.AlignmentView (alignment, csel, selection, false, true, true);\r
-jalview.datamodel.AlignmentView.summariseAlignmentView (view, System.out);\r
-} catch (e) {\r
-if (Clazz.exceptionOf (e, Exception)) {\r
-e.printStackTrace ();\r
-System.err.println ("Failed to generate alignment with selection restricted and groups marked.");\r
-} else {\r
-throw e;\r
-}\r
-}\r
-try {\r
-System.out.println ("View *with* hidden columns, no limit to selection, no groups to be collected:");\r
-view = new jalview.datamodel.AlignmentView (alignment, csel, selection, true, false, false);\r
-jalview.datamodel.AlignmentView.summariseAlignmentView (view, System.out);\r
-} catch (e) {\r
-if (Clazz.exceptionOf (e, Exception)) {\r
-e.printStackTrace ();\r
-System.err.println ("Failed to generate alignment with selection but no groups marked.");\r
-} else {\r
-throw e;\r
-}\r
-}\r
-try {\r
-System.out.println ("View *with* hidden columns, no limit to selection, and all groups to be collected:");\r
-view = new jalview.datamodel.AlignmentView (alignment, csel, selection, true, false, true);\r
-jalview.datamodel.AlignmentView.summariseAlignmentView (view, System.out);\r
-} catch (e) {\r
-if (Clazz.exceptionOf (e, Exception)) {\r
-e.printStackTrace ();\r
-System.err.println ("Failed to generate alignment with selection marked but no groups marked.");\r
-} else {\r
-throw e;\r
-}\r
-}\r
-try {\r
-System.out.println ("View *with* hidden columns, limited to selection and no groups to be collected:");\r
-view = new jalview.datamodel.AlignmentView (alignment, csel, selection, true, true, false);\r
-jalview.datamodel.AlignmentView.summariseAlignmentView (view, System.out);\r
-} catch (e) {\r
-if (Clazz.exceptionOf (e, Exception)) {\r
-e.printStackTrace ();\r
-System.err.println ("Failed to generate alignment with selection restricted but no groups marked.");\r
-} else {\r
-throw e;\r
-}\r
-}\r
-try {\r
-System.out.println ("View *with* hidden columns, limited to selection, and all groups to be collected:");\r
-view = new jalview.datamodel.AlignmentView (alignment, csel, selection, true, true, true);\r
-jalview.datamodel.AlignmentView.summariseAlignmentView (view, System.out);\r
-} catch (e) {\r
-if (Clazz.exceptionOf (e, Exception)) {\r
-e.printStackTrace ();\r
-System.err.println ("Failed to generate alignment with selection restricted and groups marked.");\r
-} else {\r
-throw e;\r
-}\r
-}\r
-}, "jalview.datamodel.AlignmentI,jalview.datamodel.ColumnSelection,jalview.datamodel.SequenceGroup");\r
-c$.$AlignmentView$ScGroup$ = function () {\r
-Clazz.pu$h ();\r
-c$ = Clazz.decorateAsClass (function () {\r
-Clazz.prepareCallback (this, arguments);\r
-this.seqs = null;\r
-this.sg = null;\r
-Clazz.instantialize (this, arguments);\r
-}, jalview.datamodel.AlignmentView, "ScGroup");\r
-Clazz.makeConstructor (c$, \r
-function () {\r
-this.seqs = new java.util.Vector ();\r
-});\r
-c$ = Clazz.p0p ();\r
-};\r
-});\r
+Clazz.declarePackage ("jalview.datamodel");
+Clazz.load (null, "jalview.datamodel.AlignmentView", ["jalview.datamodel.Alignment", "$.CigarArray", "$.ColumnSelection", "$.SeqCigar", "$.SequenceGroup", "jalview.util.MessageManager", "$.ShiftList", "java.lang.Error", "java.util.ArrayList", "$.Vector"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.sequences = null;
+this.contigs = null;
+this.width = 0;
+this.firstCol = 0;
+this.scGroups = null;
+this.$isNa = false;
+if (!Clazz.isClassDefined ("jalview.datamodel.AlignmentView.ScGroup")) {
+jalview.datamodel.AlignmentView.$AlignmentView$ScGroup$ ();
+}
+this.selected = null;
+Clazz.instantialize (this, arguments);
+}, jalview.datamodel, "AlignmentView");
+Clazz.defineMethod (c$, "isNa",
+function () {
+return this.$isNa;
+});
+Clazz.makeConstructor (c$,
+function (alignment, columnSelection, selection, hasHiddenColumns, selectedRegionOnly, recordGroups) {
+this.construct ( new jalview.datamodel.CigarArray (alignment, (hasHiddenColumns ? columnSelection : null), (selectedRegionOnly ? selection : null)), (selectedRegionOnly && selection != null) ? selection.getStartRes () : 0);
+this.$isNa = alignment.isNucleotide ();
+var selseqs;
+if (selection != null && selection.getSize () > 0) {
+var sel = selection.getSequences (null);
+this.selected = new java.util.Vector ();
+selseqs = selection.getSequencesInOrder (alignment, selectedRegionOnly);
+} else {
+selseqs = alignment.getSequencesArray ();
+}var seqsets = new java.util.ArrayList ();
+var grps = new java.util.ArrayList ();
+var gg = alignment.getGroups ();
+grps.addAll (gg);
+var sgrps = null;
+var addedgps = null;
+if (grps != null) {
+if (selection != null && selectedRegionOnly) {
+var ssel = selection.getStartRes ();
+var esel = selection.getEndRes ();
+var isg = new java.util.ArrayList ();
+for (var sg, $sg = grps.iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {
+if (!(sg.getStartRes () > esel || sg.getEndRes () < ssel)) {
+if (sg.getStartRes () < ssel) {
+sg.setStartRes (ssel);
+}if (sg.getEndRes () > esel) {
+sg.setEndRes (esel);
+}sg.setStartRes (sg.getStartRes () - ssel + 1);
+sg.setEndRes (sg.getEndRes () - ssel + 1);
+isg.add (sg);
+}}
+grps = isg;
+}sgrps = new Array (grps.size ());
+addedgps = Clazz.newBooleanArray (grps.size (), false);
+for (var g = 0; g < sgrps.length; g++) {
+var sg = grps.get (g);
+sgrps[g] = Clazz.innerTypeInstance (jalview.datamodel.AlignmentView.ScGroup, this, null);
+sgrps[g].sg = new jalview.datamodel.SequenceGroup (sg);
+addedgps[g] = false;
+seqsets.add (sg.getSequences ());
+}
+}var csi = 0;
+for (var i = 0; i < selseqs.length; i++) {
+if (selseqs[i] != null) {
+if (selection != null && selection.getSize () > 0 && !selectedRegionOnly) {
+this.sequences[csi].setGroupMembership (this.selected);
+this.selected.addElement (this.sequences[csi]);
+}if (seqsets != null) {
+for (var sg = 0; sg < sgrps.length; sg++) {
+if ((seqsets.get (sg)).contains (selseqs[i])) {
+this.sequences[csi].setGroupMembership (sgrps[sg]);
+sgrps[sg].sg.deleteSequence (selseqs[i], false);
+sgrps[sg].seqs.addElement (this.sequences[csi]);
+if (!addedgps[sg]) {
+if (this.scGroups == null) {
+this.scGroups = new java.util.ArrayList ();
+}addedgps[sg] = true;
+this.scGroups.add (sgrps[sg]);
+}}}
+}csi++;
+}}
+for (var sg = 0; sg < sgrps.length; sg++) {
+var sqs = sgrps[sg].sg.getSequencesAsArray (null);
+for (var si = 0; si < sqs.length; si++) {
+sgrps[sg].sg.deleteSequence (sqs[si], false);
+}
+sgrps[sg] = null;
+}
+}, "jalview.datamodel.AlignmentI,jalview.datamodel.ColumnSelection,jalview.datamodel.SequenceGroup,~B,~B,~B");
+Clazz.makeConstructor (c$,
+function (seqcigararray) {
+if (!seqcigararray.isSeqCigarArray ()) {
+throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_can_only_make_alignmnet_from_cigararray"));
+}this.contigs = seqcigararray.getDeletedRegions ();
+this.sequences = seqcigararray.getSeqCigarArray ();
+this.width = seqcigararray.getWidth ();
+}, "jalview.datamodel.CigarArray");
+Clazz.makeConstructor (c$,
+function (sdata, firstcol) {
+this.construct (sdata);
+this.firstCol = firstcol;
+}, "jalview.datamodel.CigarArray,~N");
+Clazz.defineMethod (c$, "setSequences",
+function (sequences) {
+this.sequences = sequences;
+}, "~A");
+Clazz.defineMethod (c$, "setContigs",
+function (contigs) {
+this.contigs = contigs;
+}, "~A");
+Clazz.defineMethod (c$, "getSequences",
+function () {
+return this.sequences;
+});
+Clazz.defineMethod (c$, "getContigs",
+function () {
+return this.contigs;
+});
+Clazz.defineMethod (c$, "getAlignmentAndColumnSelection",
+function (gapCharacter) {
+var colsel = new jalview.datamodel.ColumnSelection ();
+return Clazz.newArray (-1, [jalview.datamodel.SeqCigar.createAlignmentSequences (this.sequences, gapCharacter, colsel, this.contigs), colsel]);
+}, "~S");
+Clazz.defineMethod (c$, "getVisibleAlignment",
+function (c) {
+var aln = this.getVisibleSeqs (c);
+var vcal = new jalview.datamodel.Alignment (aln);
+this.addPrunedGroupsInOrder (vcal, -1, -1, true);
+return vcal;
+}, "~S");
+Clazz.defineMethod (c$, "addPrunedGroupsInOrder",
+($fz = function (vcal, gstart, gend, viscontigs) {
+var r = false;
+if (gstart > -1 && gstart <= gend) {
+r = true;
+}var aln = vcal.getSequencesArray ();
+{
+{
+var nvg = (this.scGroups != null) ? this.scGroups.size () : 0;
+if (nvg > 0) {
+var nsg = new Array (nvg);
+for (var g = 0; g < nvg; g++) {
+var sg = this.scGroups.get (g).sg;
+if (r) {
+if (sg.getStartRes () > gend || sg.getEndRes () < gstart) {
+nsg[g] = null;
+continue;
+}}nsg[g] = new jalview.datamodel.SequenceGroup (sg);
+if (r && !viscontigs) {
+if (nsg[g].getStartRes () < gstart) {
+nsg[g].setStartRes (0);
+} else {
+nsg[g].setStartRes (nsg[g].getStartRes () - gstart);
+nsg[g].setEndRes (nsg[g].getEndRes () - gstart);
+}if (nsg[g].getEndRes () > (gend - gstart)) {
+nsg[g].setEndRes (gend - gstart);
+}}}
+if (viscontigs) {
+if (this.contigs != null) {
+var p = 0;
+var prune = new jalview.util.ShiftList ();
+if (r) {
+prune.addShift (gstart, -gstart);
+}for (var h = 0; h < this.contigs.length; h += 3) {
+{
+prune.addShift (p + this.contigs[h + 1], this.contigs[h + 2] - this.contigs[h + 1]);
+}p = this.contigs[h + 1] + this.contigs[h + 2];
+}
+for (var g = 0; g < nsg.length; g++) {
+if (nsg[g] != null) {
+var s = nsg[g].getStartRes ();
+var t = nsg[g].getEndRes ();
+var w = 1 + t - s;
+if (r) {
+if (s < gstart) {
+s = gstart;
+}if (t > gend) {
+t = gend;
+}}s = prune.shift (s);
+t = prune.shift (t);
+nsg[g].setStartRes (s);
+nsg[g].setEndRes (t);
+}}
+}}for (var nsq = 0; nsq < aln.length; nsq++) {
+for (var g = 0; g < nvg; g++) {
+if (nsg[g] != null && this.sequences[nsq].isMemberOf (this.scGroups.get (g))) {
+nsg[g].addSequence (aln[nsq], false);
+}}
+}
+for (var g = 0; g < nvg; g++) {
+if (nsg[g] != null && nsg[g].getSize () > 0) {
+vcal.addGroup (nsg[g]);
+}nsg[g] = null;
+}
+}}}}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentI,~N,~N,~B");
+Clazz.defineMethod (c$, "getVisibleSeqs",
+($fz = function (c) {
+var aln = new Array (this.sequences.length);
+for (var i = 0, j = this.sequences.length; i < j; i++) {
+aln[i] = this.sequences[i].getSeq ('-');
+}
+var seqs = this.getSequenceStrings ('-');
+for (var i = 0, j = aln.length; i < j; i++) {
+aln[i].setSequence (seqs[i]);
+}
+return aln;
+}, $fz.isPrivate = true, $fz), "~S");
+Clazz.defineMethod (c$, "getVisibleContigAlignments",
+function (c) {
+var nvc = 0;
+var vcontigs = this.getVisibleContigs ();
+var contigviews = this.getVisibleContigs (c);
+var vcals = new Array (contigviews.length);
+for (nvc = 0; nvc < contigviews.length; nvc++) {
+vcals[nvc] = new jalview.datamodel.Alignment (contigviews[nvc]);
+if (this.scGroups != null && this.scGroups.size () > 0) {
+this.addPrunedGroupsInOrder (vcals[nvc], vcontigs[nvc * 2], vcontigs[nvc * 2 + 1], true);
+}}
+return vcals;
+}, "~S");
+Clazz.defineMethod (c$, "getSequenceStrings",
+function (c) {
+var seqs = new Array (this.sequences.length);
+for (var n = 0; n < this.sequences.length; n++) {
+var fullseq = this.sequences[n].getSequenceString (c);
+if (this.contigs != null) {
+seqs[n] = "";
+var p = 0;
+for (var h = 0; h < this.contigs.length; h += 3) {
+seqs[n] += fullseq.substring (p, this.contigs[h + 1]);
+p = this.contigs[h + 1] + this.contigs[h + 2];
+}
+seqs[n] += fullseq.substring (p);
+} else {
+seqs[n] = fullseq;
+}}
+return seqs;
+}, "~S");
+Clazz.defineMethod (c$, "getWidth",
+function () {
+return this.width;
+});
+Clazz.defineMethod (c$, "setWidth",
+function (width) {
+this.width = width;
+}, "~N");
+Clazz.defineMethod (c$, "getVisibleContigs",
+function (gapCharacter) {
+var smsa;
+var njobs = 1;
+if (this.sequences == null || this.width <= 0) {
+return null;
+}if (this.contigs != null && this.contigs.length > 0) {
+var start = 0;
+njobs = 0;
+var fwidth = this.width;
+for (var contig = 0; contig < this.contigs.length; contig += 3) {
+if ((this.contigs[contig + 1] - start) > 0) {
+njobs++;
+}fwidth += this.contigs[contig + 2];
+start = this.contigs[contig + 1] + this.contigs[contig + 2];
+}
+if (start < fwidth) {
+njobs++;
+}smsa = new Array (njobs);
+start = 0;
+var j = 0;
+for (var contig = 0; contig < this.contigs.length; contig += 3) {
+if (this.contigs[contig + 1] - start > 0) {
+var mseq = new Array (this.sequences.length);
+for (var s = 0; s < mseq.length; s++) {
+mseq[s] = this.sequences[s].getSeq (gapCharacter).getSubSequence (start, this.contigs[contig + 1]);
+}
+smsa[j] = mseq;
+j++;
+}start = this.contigs[contig + 1] + this.contigs[contig + 2];
+}
+if (start < fwidth) {
+var mseq = new Array (this.sequences.length);
+for (var s = 0; s < mseq.length; s++) {
+mseq[s] = this.sequences[s].getSeq (gapCharacter).getSubSequence (start, fwidth + 1);
+}
+smsa[j] = mseq;
+j++;
+}} else {
+smsa = new Array (1);
+smsa[0] = new Array (this.sequences.length);
+for (var s = 0; s < this.sequences.length; s++) {
+smsa[0][s] = this.sequences[s].getSeq (gapCharacter);
+}
+}return smsa;
+}, "~S");
+Clazz.defineMethod (c$, "getUpdatedView",
+function (nvismsa, orders, gapCharacter) {
+if (this.sequences == null || this.width <= 0) {
+throw new Error (jalview.util.MessageManager.getString ("error.empty_view_cannot_be_updated"));
+}if (nvismsa == null) {
+throw new Error ("nvismsa==null. use getAlignmentAndColumnSelection() instead.");
+}if (this.contigs != null && this.contigs.length > 0) {
+var alignment = new Array (this.sequences.length);
+var columnselection = new jalview.datamodel.ColumnSelection ();
+if (this.contigs != null && this.contigs.length > 0) {
+var start = 0;
+var nwidth = 0;
+var owidth = this.width;
+var j = 0;
+for (var contig = 0; contig < this.contigs.length; contig += 3) {
+owidth += this.contigs[contig + 2];
+if (this.contigs[contig + 1] - start > 0) {
+var swidth = 0;
+if (nvismsa[j] != null) {
+var mseq = nvismsa[j];
+var order = (orders == null) ? null : orders[j];
+j++;
+if (mseq.length != this.sequences.length) {
+throw new Error (jalview.util.MessageManager.formatMessage ("error.mismatch_between_number_of_sequences_in_block", Clazz.newArray (-1, [Integer.$valueOf (j).toString (), Integer.$valueOf (mseq.length).toString (), Integer.$valueOf (this.sequences.length).toString ()])));
+}swidth = mseq[0].getLength ();
+for (var s = 0; s < mseq.length; s++) {
+if (alignment[s] == null) {
+alignment[s] = mseq[s];
+} else {
+alignment[s].setSequence (alignment[s].getSequenceAsString () + mseq[s].getSequenceAsString ());
+if (mseq[s].getStart () <= mseq[s].getEnd ()) {
+alignment[s].setEnd (mseq[s].getEnd ());
+}if (order != null) {
+order.updateSequence (mseq[s], alignment[s]);
+}}}
+} else {
+if (true) {
+for (var s = 0; s < this.sequences.length; s++) {
+var oseq = this.sequences[s].getSeq (gapCharacter).getSubSequence (start, this.contigs[contig + 1]);
+if (swidth < oseq.getLength ()) {
+swidth = oseq.getLength ();
+}if (alignment[s] == null) {
+alignment[s] = oseq;
+} else {
+alignment[s].setSequence (alignment[s].getSequenceAsString () + oseq.getSequenceAsString ());
+if (oseq.getEnd () >= oseq.getStart ()) {
+alignment[s].setEnd (oseq.getEnd ());
+}}}
+}j++;
+}nwidth += swidth;
+}start = this.contigs[contig + 1] + this.contigs[contig + 2];
+for (var s = 0; s < this.sequences.length; s++) {
+var hseq = this.sequences[s].getSeq (gapCharacter).getSubSequence (this.contigs[contig + 1], start);
+if (alignment[s] == null) {
+alignment[s] = hseq;
+} else {
+alignment[s].setSequence (alignment[s].getSequenceAsString () + hseq.getSequenceAsString ());
+if (hseq.getEnd () >= hseq.getStart ()) {
+alignment[s].setEnd (hseq.getEnd ());
+}}}
+columnselection.hideColumns (nwidth, nwidth + this.contigs[contig + 2] - 1);
+nwidth += this.contigs[contig + 2];
+}
+if (j < nvismsa.length) {
+var swidth = 0;
+if (nvismsa[j] != null) {
+var mseq = nvismsa[j];
+var order = (orders != null) ? orders[j] : null;
+swidth = mseq[0].getLength ();
+for (var s = 0; s < mseq.length; s++) {
+if (alignment[s] == null) {
+alignment[s] = mseq[s];
+} else {
+alignment[s].setSequence (alignment[s].getSequenceAsString () + mseq[s].getSequenceAsString ());
+if (mseq[s].getEnd () >= mseq[s].getStart ()) {
+alignment[s].setEnd (mseq[s].getEnd ());
+}if (order != null) {
+order.updateSequence (mseq[s], alignment[s]);
+}}}
+} else {
+if (start < owidth) {
+if (true) {
+for (var s = 0; s < this.sequences.length; s++) {
+var oseq = this.sequences[s].getSeq (gapCharacter).getSubSequence (start, owidth + 1);
+if (swidth < oseq.getLength ()) {
+swidth = oseq.getLength ();
+}if (alignment[s] == null) {
+alignment[s] = oseq;
+} else {
+alignment[s].setSequence (alignment[s].getSequenceAsString () + oseq.getSequenceAsString ());
+if (oseq.getEnd () >= oseq.getStart ()) {
+alignment[s].setEnd (oseq.getEnd ());
+}}}
+nwidth += swidth;
+} else {
+throw new Error (jalview.util.MessageManager.getString ("error.padding_not_yet_implemented"));
+}}}}}return Clazz.newArray (-1, [alignment, columnselection]);
+} else {
+if (nvismsa.length != 1) {
+throw new Error (jalview.util.MessageManager.formatMessage ("error.mismatch_between_visible_blocks_to_update_and_number_of_contigs_in_view", Clazz.newArray (-1, [Integer.$valueOf (nvismsa.length).toString ()])));
+}if (nvismsa[0] != null) {
+return Clazz.newArray (-1, [nvismsa[0], new jalview.datamodel.ColumnSelection ()]);
+} else {
+return this.getAlignmentAndColumnSelection (gapCharacter);
+}}}, "~A,~A,~S");
+Clazz.defineMethod (c$, "getVisibleContigs",
+function () {
+if (this.contigs != null && this.contigs.length > 0) {
+var start = 0;
+var nvis = 0;
+var fwidth = this.width;
+for (var contig = 0; contig < this.contigs.length; contig += 3) {
+if ((this.contigs[contig + 1] - start) > 0) {
+nvis++;
+}fwidth += this.contigs[contig + 2];
+start = this.contigs[contig + 1] + this.contigs[contig + 2];
+}
+if (start < fwidth) {
+nvis++;
+}var viscontigs = Clazz.newIntArray (nvis * 2, 0);
+nvis = 0;
+start = 0;
+for (var contig = 0; contig < this.contigs.length; contig += 3) {
+if ((this.contigs[contig + 1] - start) > 0) {
+viscontigs[nvis] = start;
+viscontigs[nvis + 1] = this.contigs[contig + 1] - 1;
+nvis += 2;
+}start = this.contigs[contig + 1] + this.contigs[contig + 2];
+}
+if (start < fwidth) {
+viscontigs[nvis] = start;
+viscontigs[nvis + 1] = fwidth;
+nvis += 2;
+}return viscontigs;
+} else {
+return Clazz.newIntArray (-1, [0, this.width]);
+}});
+Clazz.defineMethod (c$, "getAlignmentOrigin",
+function () {
+return this.firstCol;
+});
+Clazz.defineMethod (c$, "getVisibleContigMapFor",
+function (gapMap) {
+var delMap = null;
+var viscontigs = this.getVisibleContigs ();
+var spos = 0;
+var i = 0;
+if (viscontigs != null) {
+delMap = Clazz.newIntArray (gapMap.length, 0);
+for (var contig = 0; contig < viscontigs.length; contig += 2) {
+while (spos < gapMap.length && gapMap[spos] < viscontigs[contig]) {
+spos++;
+}
+while (spos < gapMap.length && gapMap[spos] <= viscontigs[contig + 1]) {
+delMap[i++] = spos++;
+}
+}
+var tmap = Clazz.newIntArray (i, 0);
+System.arraycopy (delMap, 0, tmap, 0, i);
+delMap = tmap;
+}return delMap;
+}, "~A");
+Clazz.defineMethod (c$, "getEditedSequences",
+function (gc, $delete) {
+var msf = this.getSequences ();
+var aln = new Array (msf.length);
+for (var i = 0, j = msf.length; i < j; i++) {
+aln[i] = msf[i].getSeq (gc);
+}
+if ($delete) {
+var sqs = this.getSequenceStrings (gc);
+for (var i = 0; i < sqs.length; i++) {
+aln[i].setSequence (sqs[i]);
+sqs[i] = null;
+}
+}return aln;
+}, "~S,~B");
+c$.summariseAlignmentView = Clazz.defineMethod (c$, "summariseAlignmentView",
+function (view, os) {
+os.print ("View has " + view.sequences.length + " of which ");
+if (view.selected == null) {
+os.print ("None");
+} else {
+os.print (" " + view.selected.size ());
+}os.println (" are selected.");
+os.print ("View is " + view.getWidth () + " columns wide");
+var viswid = 0;
+var contigs = view.getContigs ();
+if (contigs != null) {
+viswid = view.width;
+for (var i = 0; i < contigs.length; i += 3) {
+viswid += contigs[i + 2];
+}
+os.println ("with " + viswid + " visible columns spread over " + Clazz.doubleToInt (contigs.length / 3) + " regions.");
+} else {
+viswid = view.width;
+os.println (".");
+}if (view.scGroups != null) {
+os.println ("There are " + view.scGroups.size () + " groups defined on the view.");
+for (var g = 0; g < view.scGroups.size (); g++) {
+var sgr = view.scGroups.get (g);
+os.println ("Group " + g + ": Name = " + sgr.sg.getName () + " Contains " + sgr.seqs.size () + " Seqs.");
+os.println ("This group runs from " + sgr.sg.getStartRes () + " to " + sgr.sg.getEndRes ());
+for (var s = 0; s < sgr.seqs.size (); s++) {
+if (!(sgr.seqs.elementAt (s)).isMemberOf (sgr)) {
+os.println ("** WARNING: sequence " + (sgr.seqs.elementAt (s)).toString () + " is not marked as member of group.");
+}}
+}
+var visal = view.getVisibleAlignment ('-');
+if (visal != null) {
+os.println ("Vis. alignment is " + visal.getWidth () + " wide and has " + visal.getHeight () + " seqs.");
+if (visal.getGroups () != null && visal.getGroups ().size () > 0) {
+var i = 1;
+for (var sg, $sg = visal.getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {
+os.println ("Group " + (i++) + " begins at column " + sg.getStartRes () + " and ends at " + sg.getEndRes ());
+}
+}}}}, "jalview.datamodel.AlignmentView,java.io.PrintStream");
+c$.testSelectionViews = Clazz.defineMethod (c$, "testSelectionViews",
+function (alignment, csel, selection) {
+System.out.println ("Testing standard view creation:\n");
+var view = null;
+try {
+System.out.println ("View with no hidden columns, no limit to selection, no groups to be collected:");
+view = new jalview.datamodel.AlignmentView (alignment, csel, selection, false, false, false);
+jalview.datamodel.AlignmentView.summariseAlignmentView (view, System.out);
+} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+e.printStackTrace ();
+System.err.println ("Failed to generate alignment with selection but no groups marked.");
+} else {
+throw e;
+}
+}
+try {
+System.out.println ("View with no hidden columns, no limit to selection, and all groups to be collected:");
+view = new jalview.datamodel.AlignmentView (alignment, csel, selection, false, false, true);
+jalview.datamodel.AlignmentView.summariseAlignmentView (view, System.out);
+} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+e.printStackTrace ();
+System.err.println ("Failed to generate alignment with selection marked but no groups marked.");
+} else {
+throw e;
+}
+}
+try {
+System.out.println ("View with no hidden columns, limited to selection and no groups to be collected:");
+view = new jalview.datamodel.AlignmentView (alignment, csel, selection, false, true, false);
+jalview.datamodel.AlignmentView.summariseAlignmentView (view, System.out);
+} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+e.printStackTrace ();
+System.err.println ("Failed to generate alignment with selection restricted but no groups marked.");
+} else {
+throw e;
+}
+}
+try {
+System.out.println ("View with no hidden columns, limited to selection, and all groups to be collected:");
+view = new jalview.datamodel.AlignmentView (alignment, csel, selection, false, true, true);
+jalview.datamodel.AlignmentView.summariseAlignmentView (view, System.out);
+} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+e.printStackTrace ();
+System.err.println ("Failed to generate alignment with selection restricted and groups marked.");
+} else {
+throw e;
+}
+}
+try {
+System.out.println ("View *with* hidden columns, no limit to selection, no groups to be collected:");
+view = new jalview.datamodel.AlignmentView (alignment, csel, selection, true, false, false);
+jalview.datamodel.AlignmentView.summariseAlignmentView (view, System.out);
+} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+e.printStackTrace ();
+System.err.println ("Failed to generate alignment with selection but no groups marked.");
+} else {
+throw e;
+}
+}
+try {
+System.out.println ("View *with* hidden columns, no limit to selection, and all groups to be collected:");
+view = new jalview.datamodel.AlignmentView (alignment, csel, selection, true, false, true);
+jalview.datamodel.AlignmentView.summariseAlignmentView (view, System.out);
+} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+e.printStackTrace ();
+System.err.println ("Failed to generate alignment with selection marked but no groups marked.");
+} else {
+throw e;
+}
+}
+try {
+System.out.println ("View *with* hidden columns, limited to selection and no groups to be collected:");
+view = new jalview.datamodel.AlignmentView (alignment, csel, selection, true, true, false);
+jalview.datamodel.AlignmentView.summariseAlignmentView (view, System.out);
+} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+e.printStackTrace ();
+System.err.println ("Failed to generate alignment with selection restricted but no groups marked.");
+} else {
+throw e;
+}
+}
+try {
+System.out.println ("View *with* hidden columns, limited to selection, and all groups to be collected:");
+view = new jalview.datamodel.AlignmentView (alignment, csel, selection, true, true, true);
+jalview.datamodel.AlignmentView.summariseAlignmentView (view, System.out);
+} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+e.printStackTrace ();
+System.err.println ("Failed to generate alignment with selection restricted and groups marked.");
+} else {
+throw e;
+}
+}
+}, "jalview.datamodel.AlignmentI,jalview.datamodel.ColumnSelection,jalview.datamodel.SequenceGroup");
+c$.$AlignmentView$ScGroup$ = function () {
+Clazz.pu$h ();
+c$ = Clazz.decorateAsClass (function () {
+Clazz.prepareCallback (this, arguments);
+this.seqs = null;
+this.sg = null;
+Clazz.instantialize (this, arguments);
+}, jalview.datamodel.AlignmentView, "ScGroup");
+Clazz.makeConstructor (c$,
+function () {
+this.seqs = new java.util.Vector ();
+});
+c$ = Clazz.p0p ();
+};
+});
git://source.jalview.org / jalviewjs.git / blobdiff