Revision f2218c81
Added by Ben Stöver over 8 years ago
| eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/editor/AlignmentEditor.java | ||
|---|---|---|
| 692 | 692 |
|
| 693 | 693 |
if (tokens != null) { // If either an edited sequence or a pherogram URI was provided.
|
| 694 | 694 |
provider.insertTokensAt(id, 0, tokens); |
| 695 |
// Create pherogram area: |
|
| 696 |
PherogramArea pherogramArea = new PherogramArea(getReadsArea().getContentArea(), |
|
| 697 |
new PherogramAreaModel(pherogramProvider)); |
|
| 698 |
|
|
| 699 |
// Set position properties and shifts: |
|
| 700 |
PherogramAreaModel model = pherogramArea.getModel(); |
|
| 701 |
if ((firstSeqPos != null) && (leftCutPos != null)) {
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|
| 702 |
model.setFirstSeqLeftCutPos(firstSeqPos, leftCutPos); |
|
| 703 |
} |
|
| 704 |
if (rightCutPos != null) {
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|
| 705 |
model.setRightCutPosition(rightCutPos); |
|
| 706 |
} |
|
| 707 |
if ((shifts != null) && (shifts.length > 0)) {
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|
| 708 |
for (int i = 0; i < shifts.length; i++) {
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|
| 709 |
model.addShiftChange(shifts[i].position, shifts[i].shift); |
|
| 710 |
} |
|
| 711 |
setDirty(); |
|
| 712 |
} |
|
| 713 |
|
|
| 714 |
// Add pherogram area to GUI: |
|
| 715 |
pherogramArea.addMouseListener(new PherogramMouseListener(pherogramArea)); |
|
| 716 |
getReadsArea().getDataAreas().getSequenceAreas(id).add(pherogramArea); |
|
| 717 |
} |
|
| 695 |
|
|
| 696 |
if (pherogramProvider != null) {
|
|
| 697 |
// Create pherogram area: |
|
| 698 |
PherogramArea pherogramArea = new PherogramArea(getReadsArea().getContentArea(), |
|
| 699 |
new PherogramAreaModel(pherogramProvider)); |
|
| 700 |
|
|
| 701 |
// Set position properties and shifts: |
|
| 702 |
PherogramAreaModel model = pherogramArea.getModel(); |
|
| 703 |
if ((firstSeqPos != null) && (leftCutPos != null)) {
|
|
| 704 |
model.setFirstSeqLeftCutPos(firstSeqPos, leftCutPos); |
|
| 705 |
} |
|
| 706 |
if (rightCutPos != null) {
|
|
| 707 |
model.setRightCutPosition(rightCutPos); |
|
| 708 |
} |
|
| 709 |
if ((shifts != null) && (shifts.length > 0)) {
|
|
| 710 |
for (int i = 0; i < shifts.length; i++) {
|
|
| 711 |
model.addShiftChange(shifts[i].position, shifts[i].shift); |
|
| 712 |
} |
|
| 713 |
setDirty(); |
|
| 714 |
} |
|
| 718 | 715 |
|
| 716 |
// Add pherogram area to GUI: |
|
| 717 |
pherogramArea.addMouseListener(new PherogramMouseListener(pherogramArea)); |
|
| 718 |
getReadsArea().getDataAreas().getSequenceAreas(id).add(pherogramArea); |
|
| 719 |
} |
|
| 720 |
} |
|
| 719 | 721 |
return id; |
| 720 | 722 |
} |
| 721 | 723 |
} |
Also available in: Unified diff
Fixed NPE when loading single reads without attached pherogram.