X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentView.java;h=6ab71c74530268fe5f7427156cfe077813d23a9c;hb=HEAD;hp=5058dcff0de4b547e867154b7296330f3840dea0;hpb=e5b2edf3955c50cfd61799ad12cdc9016603ee1c;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java index 5058dcf..6ab71c7 100644 --- a/src/jalview/datamodel/AlignmentView.java +++ b/src/jalview/datamodel/AlignmentView.java @@ -74,7 +74,7 @@ public class AlignmentView ScGroup() { - seqs = new ArrayList(); + seqs = new ArrayList<>(); } /** @@ -140,18 +140,17 @@ public class AlignmentView * - when set, any groups on the given alignment will be marked on * the view */ - public AlignmentView(AlignmentI alignment, - HiddenColumns hidden, - SequenceGroup selection, - boolean hasHiddenColumns, boolean selectedRegionOnly, - boolean recordGroups) + public AlignmentView(AlignmentI alignment, HiddenColumns hidden, + SequenceGroup selection, boolean hasHiddenColumns, + boolean selectedRegionOnly, boolean recordGroups) { // refactored from AlignViewport.getAlignmentView(selectedOnly); this(new jalview.datamodel.CigarArray(alignment, (hasHiddenColumns ? hidden : null), (selectedRegionOnly ? selection : null)), - (selectedRegionOnly && selection != null) ? selection - .getStartRes() : 0); + (selectedRegionOnly && selection != null) + ? selection.getStartRes() + : 0); isNa = alignment.isNucleotide(); // walk down SeqCigar array and Alignment Array - optionally restricted by // selected region. @@ -161,19 +160,18 @@ public class AlignmentView SequenceI[] selseqs; if (selection != null && selection.getSize() > 0) { - List sel = selection.getSequences(null); this.selected = new ScGroup(); - selseqs = selection - .getSequencesInOrder(alignment, selectedRegionOnly); + selseqs = selection.getSequencesInOrder(alignment, + selectedRegionOnly); } else { selseqs = alignment.getSequencesArray(); } - List> seqsets = new ArrayList>(); + List> seqsets = new ArrayList<>(); // get the alignment's group list and make a copy - List grps = new ArrayList(); + List grps = new ArrayList<>(); List gg = alignment.getGroups(); grps.addAll(gg); ScGroup[] sgrps = null; @@ -186,7 +184,7 @@ public class AlignmentView // strip out any groups that do not actually intersect with the // visible and selected region int ssel = selection.getStartRes(), esel = selection.getEndRes(); - List isg = new ArrayList(); + List isg = new ArrayList<>(); for (SequenceGroup sg : grps) { if (!(sg.getStartRes() > esel || sg.getEndRes() < ssel)) @@ -246,7 +244,7 @@ public class AlignmentView { if (scGroups == null) { - scGroups = new ArrayList(); + scGroups = new ArrayList<>(); } addedgps[sg] = true; scGroups.add(sgrps[sg]); @@ -335,9 +333,9 @@ public class AlignmentView { HiddenColumns hidden = new HiddenColumns(); - return new Object[] { - SeqCigar.createAlignmentSequences(sequences, gapCharacter, hidden, - contigs), hidden }; + return new Object[] { SeqCigar.createAlignmentSequences(sequences, + gapCharacter, hidden, contigs), + hidden }; } /** @@ -370,8 +368,8 @@ public class AlignmentView * - true if vcal is alignment of the visible regions of the view * (e.g. as returned from getVisibleAlignment) */ - private void addPrunedGroupsInOrder(AlignmentI vcal, int gstart, - int gend, boolean viscontigs) + private void addPrunedGroupsInOrder(AlignmentI vcal, int gstart, int gend, + boolean viscontigs) { boolean r = false; if (gstart > -1 && gstart <= gend) @@ -441,8 +439,8 @@ public class AlignmentView for (int h = 0; h < contigs.length; h += 3) { { - prune.addShift(p + contigs[h + 1], contigs[h + 2] - - contigs[h + 1]); + prune.addShift(p + contigs[h + 1], + contigs[h + 2] - contigs[h + 1]); } p = contigs[h + 1] + contigs[h + 2]; } @@ -652,8 +650,8 @@ public class AlignmentView SequenceI mseq[] = new SequenceI[sequences.length]; for (int s = 0; s < mseq.length; s++) { - mseq[s] = sequences[s].getSeq(gapCharacter).getSubSequence( - start, contigs[contig + 1]); + mseq[s] = sequences[s].getSeq(gapCharacter) + .getSubSequence(start, contigs[contig + 1]); } smsa[j] = mseq; j++; @@ -699,9 +697,8 @@ public class AlignmentView { if (sequences == null || width <= 0) { - throw new Error( - MessageManager - .getString("error.empty_view_cannot_be_updated")); + throw new Error(MessageManager + .getString("error.empty_view_cannot_be_updated")); } if (nvismsa == null) { @@ -732,17 +729,13 @@ public class AlignmentView j++; if (mseq.length != sequences.length) { - throw new Error( - MessageManager - .formatMessage( - "error.mismatch_between_number_of_sequences_in_block", - new String[] { - Integer.valueOf(j).toString(), - Integer.valueOf(mseq.length) - .toString(), - Integer.valueOf( - sequences.length) - .toString() })); + throw new Error(MessageManager.formatMessage( + "error.mismatch_between_number_of_sequences_in_block", + new String[] + { Integer.valueOf(j).toString(), + Integer.valueOf(mseq.length).toString(), + Integer.valueOf(sequences.length) + .toString() })); } swidth = mseq[0].getLength(); // JBPNote: could ensure padded // here. @@ -754,9 +747,9 @@ public class AlignmentView } else { - alignment[s].setSequence(alignment[s] - .getSequenceAsString() - + mseq[s].getSequenceAsString()); + alignment[s] + .setSequence(alignment[s].getSequenceAsString() + + mseq[s].getSequenceAsString()); if (mseq[s].getStart() <= mseq[s].getEnd()) { alignment[s].setEnd(mseq[s].getEnd()); @@ -788,9 +781,9 @@ public class AlignmentView } else { - alignment[s].setSequence(alignment[s] - .getSequenceAsString() - + oseq.getSequenceAsString()); + alignment[s] + .setSequence(alignment[s].getSequenceAsString() + + oseq.getSequenceAsString()); if (oseq.getEnd() >= oseq.getStart()) { alignment[s].setEnd(oseq.getEnd()); @@ -825,8 +818,7 @@ public class AlignmentView } } // mark hidden segment as hidden in the new alignment - hidden.hideColumns(nwidth, nwidth + contigs[contig + 2] - - 1); + hidden.hideColumns(nwidth, nwidth + contigs[contig + 2] - 1); nwidth += contigs[contig + 2]; } // Do final segment - if it exists @@ -881,9 +873,9 @@ public class AlignmentView } else { - alignment[s].setSequence(alignment[s] - .getSequenceAsString() - + oseq.getSequenceAsString()); + alignment[s] + .setSequence(alignment[s].getSequenceAsString() + + oseq.getSequenceAsString()); if (oseq.getEnd() >= oseq.getStart()) { alignment[s].setEnd(oseq.getEnd()); @@ -895,9 +887,8 @@ public class AlignmentView else { // place gaps. - throw new Error( - MessageManager - .getString("error.padding_not_yet_implemented")); + throw new Error(MessageManager + .getString("error.padding_not_yet_implemented")); } } } @@ -909,16 +900,14 @@ public class AlignmentView { if (nvismsa.length != 1) { - throw new Error( - MessageManager - .formatMessage( - "error.mismatch_between_visible_blocks_to_update_and_number_of_contigs_in_view", - new String[] { Integer.valueOf( - nvismsa.length).toString() })); + throw new Error(MessageManager.formatMessage( + "error.mismatch_between_visible_blocks_to_update_and_number_of_contigs_in_view", + new String[] + { Integer.valueOf(nvismsa.length).toString() })); } if (nvismsa[0] != null) { - return new Object[] { nvismsa[0], new ColumnSelection() }; + return new Object[] { nvismsa[0], new HiddenColumns() }; } else { @@ -1139,12 +1128,12 @@ public class AlignmentView public static void testSelectionViews(AlignmentI alignment, HiddenColumns hidden, SequenceGroup selection) { - System.out.println("Testing standard view creation:\n"); + jalview.bin.Console.outPrintln("Testing standard view creation:\n"); AlignmentView view = null; try { - System.out - .println("View with no hidden columns, no limit to selection, no groups to be collected:"); + jalview.bin.Console.outPrintln( + "View with no hidden columns, no limit to selection, no groups to be collected:"); view = new AlignmentView(alignment, hidden, selection, false, false, false); summariseAlignmentView(view, System.out); @@ -1152,99 +1141,99 @@ public class AlignmentView } catch (Exception e) { e.printStackTrace(); - System.err - .println("Failed to generate alignment with selection but no groups marked."); + jalview.bin.Console.errPrintln( + "Failed to generate alignment with selection but no groups marked."); } try { - System.out - .println("View with no hidden columns, no limit to selection, and all groups to be collected:"); + jalview.bin.Console.outPrintln( + "View with no hidden columns, no limit to selection, and all groups to be collected:"); view = new AlignmentView(alignment, hidden, selection, false, false, true); summariseAlignmentView(view, System.out); } catch (Exception e) { e.printStackTrace(); - System.err - .println("Failed to generate alignment with selection marked but no groups marked."); + jalview.bin.Console.errPrintln( + "Failed to generate alignment with selection marked but no groups marked."); } try { - System.out - .println("View with no hidden columns, limited to selection and no groups to be collected:"); + jalview.bin.Console.outPrintln( + "View with no hidden columns, limited to selection and no groups to be collected:"); view = new AlignmentView(alignment, hidden, selection, false, true, false); summariseAlignmentView(view, System.out); } catch (Exception e) { e.printStackTrace(); - System.err - .println("Failed to generate alignment with selection restricted but no groups marked."); + jalview.bin.Console.errPrintln( + "Failed to generate alignment with selection restricted but no groups marked."); } try { - System.out - .println("View with no hidden columns, limited to selection, and all groups to be collected:"); + jalview.bin.Console.outPrintln( + "View with no hidden columns, limited to selection, and all groups to be collected:"); view = new AlignmentView(alignment, hidden, selection, false, true, true); summariseAlignmentView(view, System.out); } catch (Exception e) { e.printStackTrace(); - System.err - .println("Failed to generate alignment with selection restricted and groups marked."); + jalview.bin.Console.errPrintln( + "Failed to generate alignment with selection restricted and groups marked."); } try { - System.out - .println("View *with* hidden columns, no limit to selection, no groups to be collected:"); + jalview.bin.Console.outPrintln( + "View *with* hidden columns, no limit to selection, no groups to be collected:"); view = new AlignmentView(alignment, hidden, selection, true, false, false); summariseAlignmentView(view, System.out); } catch (Exception e) { e.printStackTrace(); - System.err - .println("Failed to generate alignment with selection but no groups marked."); + jalview.bin.Console.errPrintln( + "Failed to generate alignment with selection but no groups marked."); } try { - System.out - .println("View *with* hidden columns, no limit to selection, and all groups to be collected:"); + jalview.bin.Console.outPrintln( + "View *with* hidden columns, no limit to selection, and all groups to be collected:"); view = new AlignmentView(alignment, hidden, selection, true, false, true); summariseAlignmentView(view, System.out); } catch (Exception e) { e.printStackTrace(); - System.err - .println("Failed to generate alignment with selection marked but no groups marked."); + jalview.bin.Console.errPrintln( + "Failed to generate alignment with selection marked but no groups marked."); } try { - System.out - .println("View *with* hidden columns, limited to selection and no groups to be collected:"); + jalview.bin.Console.outPrintln( + "View *with* hidden columns, limited to selection and no groups to be collected:"); view = new AlignmentView(alignment, hidden, selection, true, true, false); summariseAlignmentView(view, System.out); } catch (Exception e) { e.printStackTrace(); - System.err - .println("Failed to generate alignment with selection restricted but no groups marked."); + jalview.bin.Console.errPrintln( + "Failed to generate alignment with selection restricted but no groups marked."); } try { - System.out - .println("View *with* hidden columns, limited to selection, and all groups to be collected:"); + jalview.bin.Console.outPrintln( + "View *with* hidden columns, limited to selection, and all groups to be collected:"); view = new AlignmentView(alignment, hidden, selection, true, true, true); summariseAlignmentView(view, System.out); } catch (Exception e) { e.printStackTrace(); - System.err - .println("Failed to generate alignment with selection restricted and groups marked."); + jalview.bin.Console.errPrintln( + "Failed to generate alignment with selection restricted and groups marked."); } }