Examples of org.broad.igv.ui.panel.ReferenceFrame.jumpTo()

Class org.broad.igv.ui.panel.ReferenceFrame

Examples of org.broad.igv.ui.panel.ReferenceFrame.jumpTo()

org.broad.igv.ui.panel.ReferenceFrame.jumpTo()
Move the frame to the specified position. New zoom is calculated based on limits. @param chr @param start @param end


        int lastStart = genome.getChromosome(chr).getLength() - 4 * halfwidth;
        int[] starts = new int[]{500, 5000, 15000, start, 500000, lastStart};
        int[] ends = new int[]{600, 10000, 20000, end, 600000, lastStart + 2 * halfwidth};
        for (int ii = 0; ii < starts.length; ii++) {
            frame.jumpTo(new Locus(chr, starts[ii], ends[ii]));
            int actEnd = (int) frame.getEnd();


            manager.load(context, renderOptions, false);


            assertManagerHasInterval(manager, chr, starts[ii], actEnd);

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        RenderContextImpl context = new RenderContextImpl(null, null, frame, null);


        for (int pp = 0; pp < numPans; pp++) {
            shift = pp * panInterval;
            Locus locus = new Locus(chr, start + shift, end + shift);
            frame.jumpTo(locus);


            manager.load(context, renderOptions, false);


            assertManagerHasInterval(manager, chr, locus.getStart(), locus.getEnd());
        }

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        String chr = "chr1";
        int start = 5;
        int end = 5000;
        int limit = 2;


        frame.jumpTo(chr, start, end);


        Assert.assertEquals(chr, frame.getChrName());
        assertTrue(Math.abs(frame.getCurrentRange().getStart() - start) < limit);
        assertTrue(Math.abs(frame.getCurrentRange().getEnd() - end) < limit);

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            if (!chr.equals(frame.getChrName())) {
                // Switch chromosomes.  We have to do some tricks to maintain the same resolution scale.
                double range = frame.getEnd() - frame.getOrigin();
                int newOrigin = (int) Math.max(newCenter - range / 2, 0);
                int newEnd = (int) (newOrigin + range);
                frame.jumpTo(chr, newOrigin, newEnd);
            } else {
                frame.centerOnLocation(newCenter);
            }
        }
    }

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                            final String endString =
                                    getAttribute((Element) childNode, SessionAttribute.END.getText()).replace(",", "");
                            int start = ParsingUtils.parseInt(startString);
                            int end = ParsingUtils.parseInt(endString);
                            org.broad.igv.feature.Locus locus = new Locus(chr, start, end);
                            f.jumpTo(locus);
                        } catch (NumberFormatException e) {
                            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
                        }
                    }

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                    if (!chr.equals(frame.getChrName())) {
                        // Switch chromosomes.  We have to do some tricks to maintain the same resolution scale.
                        double range = frame.getEnd() - frame.getOrigin();
                        int newOrigin = (int) Math.max(newCenter - range / 2, 0);
                        int newEnd = (int) (newOrigin + range);
                        frame.jumpTo(chr, newOrigin, newEnd);
                    } else {
                        frame.centerOnLocation(newCenter);
                    }
                }
            } catch (IOException e) {

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