Package org.broad.igv.feature.genome

Examples of org.broad.igv.feature.genome.GenomeListItem

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    }

    private void removeById(String id){
        int ci = 0;
        for(; ci < this.allListItems.size(); ci++){
            GenomeListItem gli = this.allListItems.get(ci);
            if(gli.getId().equals(id)){
                break;
            }
        }
        if(ci < this.allListItems.size()) this.allListItems.remove(ci);
    }
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            if (genomeItemList.isEmpty()) {
                JOptionPane.showMessageDialog(IGV.getMainFrame(),
                        "There are no imported genomes to remove.");
            } else {

                GenomeListItem currentlySelectedDropdownGenome = IGV.getInstance().getGenomeSelectedInDropdown();
                List<String> genomeNames = new ArrayList();
                UserDefinedGenomeCheckList checkList = new UserDefinedGenomeCheckList(false);
                for (GenomeListItem genomeListItem : genomeItemList) {
                    genomeNames.add(genomeListItem.getDisplayableName());
                }
                checkList.addItems(genomeNames);
                checkList.sort();
                int status = JOptionPane.showConfirmDialog(IGV.getMainFrame(), checkList,
                        "Imported Genomes to Remove", JOptionPane.OK_CANCEL_OPTION,
                        JOptionPane.PLAIN_MESSAGE, null);

                if ((status == JOptionPane.CANCEL_OPTION) || (status == JOptionPane.CLOSED_OPTION)) {
                    return;
                }

                boolean removed = false;
                HashSet<String> selectedGenomes = checkList.getSelectedGenomes();
                Iterator iterator = genomeItemList.iterator();
                while (iterator.hasNext()) {
                    String genomeName = ((GenomeListItem) iterator.next()).getDisplayableName();

                    // Skip genome if not selected for removal
                    if (!selectedGenomes.contains(genomeName)) {
                        continue;
                    }

                    if (currentlySelectedDropdownGenome.getDisplayableName().equalsIgnoreCase(genomeName)) {
                        JOptionPane.showMessageDialog(
                                IGV.getMainFrame(),
                                "<html>Genome [" + genomeName + "] is currently in use and cannot be removed." +
                                        "<br>Please select another genome to view before trying to remove it.</html>");
                        continue;
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                }
                //We need to account for the fact that the proper
                //insertion location is one smaller, once the item being moved
                //is removed.
                if (toIndex > fromIndex) toIndex--;
                GenomeListItem item = allListItems.remove(fromIndex);
                allListItems.add(toIndex, item);
                numMoved++;
                //Account for adding multiple items, want to add them to successive indices
                toIndex++;
            }
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        @Override
        public Component getListCellRendererComponent(JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) {

            JLabel comp = new JLabel(value.toString());

            GenomeListItem item = (GenomeListItem) value;
            String displayableName = item.getDisplayableName();

            comp.setToolTipText(item.getLocation());
            if (isSelected) {
                comp.setBackground(genomeList.getSelectionBackground());
                comp.setForeground(genomeList.getSelectionForeground());
                comp.setOpaque(isSelected);
            }

            if(item.hasDownloadedSequence()){
                displayableName += LOCAL_SEQUENCE_CHAR;
            }

            comp.setText(displayableName);
            return comp;
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            }
        }
        errorWriter.println("Attempted to load " + count + " genomes");
        errorWriter.println(failedGenomes.size() + " of them failed");
        for (Map.Entry<GenomeListItem, Exception> entry : failedGenomes.entrySet()) {
            GenomeListItem item = entry.getKey();
            System.out.println(String.format("Exception loading (%s\t%s\t%s): %s", item.getDisplayableName(),
                    item.getLocation(), item.getId(), entry.getValue()));
        }

        assertEquals(0, failedGenomes.size());
    }
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            if (found) {
                refreshGenomeListComboBox();
            }
        }
        // Now select this item in the comboBox
        GenomeListItem matchingItem = GenomeManager.getInstance().getLoadedGenomeListItemById(genomeId);
        if (matchingItem != null) {
            genomeComboBox.setSelectedItem(matchingItem);
        }
    }
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        public void actionPerformed(ActionEvent actionEvent) {
            Object selItem = genomeComboBox.getSelectedItem();
            if (!(selItem instanceof GenomeListItem)) {
                return;
            }
            GenomeListItem genomeListItem = (GenomeListItem) selItem;
            loadGenomeListItem(genomeListItem);
        }
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    private void setGenome(String genomeId) {

        if (genomeId != null && !genomeId.equals(GenomeManager.getInstance().getGenomeId())) {
            try {
                GenomeListItem item = GenomeManager.getInstance().findGenomeListItemById(genomeId);
                if (item != null) {
                    IGV.getInstance().loadGenomeById(genomeId);
                }
            } catch (IOException e) {
                e.printStackTrace();
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Related Classes of org.broad.igv.feature.genome.GenomeListItem

  • org.broad.igv.data.HostedDataTest
  • org.broad.igv.ga4gh.Ga4ghLoadDialog
  • org.broad.igv.ui.action.RemoveUserDefinedGenomeMenuAction
  • org.broad.igv.ui.GenomeSelectionDialog
  • org.broad.igv.ui.IGVCommandBar
  • org.broad.igv.ui.IGVCommandBar$GenomeBoxActionListener
  • org.broad.igv.ui.ManageGenomesDialog$GenomeCellRenderer
  • org.broad.igv.ui.ManageGenomesDialog$SimpleTransferHandler
  • java.io.File
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