+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.appletgui;
-
-import jalview.datamodel.SequenceI;
-import jalview.viewmodel.OverviewDimensions;
-import jalview.datamodel.AlignmentI;
-import jalview.renderer.seqfeatures.FeatureColourFinder;
-
-import java.awt.Color;
-import java.awt.Dimension;
-import java.awt.Frame;
-import java.awt.Graphics;
-import java.awt.Image;
-import java.awt.Panel;
-import java.awt.event.ComponentAdapter;
-import java.awt.event.ComponentEvent;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.awt.event.MouseMotionListener;
-
-public class OverviewPanel extends Panel implements Runnable,
- MouseMotionListener, MouseListener
-{
- private OverviewDimensions od;
-
- private Image miniMe;
-
- private Image offscreen;
-
- private AlignViewport av;
-
- private AlignmentPanel ap;
-
- private boolean resizing = false;
-
- // This is set true if the user resizes whilst
- // the overview is being calculated
- private boolean resizeAgain = false;
-
- // Can set different properties in this seqCanvas than
- // main visible SeqCanvas
- private SequenceRenderer sr;
-
- private FeatureRenderer fr;
-
- private Frame nullFrame;
-
- public OverviewPanel(AlignmentPanel alPanel)
- {
- this.av = alPanel.av;
- this.ap = alPanel;
- setLayout(null);
- nullFrame = new Frame();
- nullFrame.addNotify();
-
- sr = new SequenceRenderer(av);
- sr.graphics = nullFrame.getGraphics();
- sr.renderGaps = false;
- sr.forOverview = true;
- fr = new FeatureRenderer(av);
-
- od = new OverviewDimensions(av.getRanges(), av.isShowAnnotation());
-
- setSize(new Dimension(od.getWidth(), od.getHeight()));
- addComponentListener(new ComponentAdapter()
- {
-
- @Override
- public void componentResized(ComponentEvent evt)
- {
- if ((getWidth() != od.getWidth())
- || (getHeight() != (od.getHeight())))
- {
- updateOverviewImage();
- }
- }
- });
-
- addMouseMotionListener(this);
-
- addMouseListener(this);
-
- updateOverviewImage();
-
- }
-
- @Override
- public void mouseEntered(MouseEvent evt)
- {
- }
-
- @Override
- public void mouseExited(MouseEvent evt)
- {
- }
-
- @Override
- public void mouseClicked(MouseEvent evt)
- {
- }
-
- @Override
- public void mouseMoved(MouseEvent evt)
- {
- }
-
- @Override
- public void mousePressed(MouseEvent evt)
- {
- mouseAction(evt);
- }
-
- @Override
- public void mouseReleased(MouseEvent evt)
- {
- mouseAction(evt);
- }
-
- @Override
- public void mouseDragged(MouseEvent evt)
- {
- mouseAction(evt);
- }
-
- private void mouseAction(MouseEvent evt)
- {
- od.updateViewportFromMouse(evt.getX(), evt.getY(), av.getAlignment()
- .getHiddenSequences(), av.getColumnSelection(), av
- .getRanges());
- ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
- ap.paintAlignment(false);
- }
-
- /**
- * Updates the overview image when the related alignment panel is updated
- */
- public void updateOverviewImage()
- {
- if (resizing)
- {
- resizeAgain = true;
- return;
- }
-
- if (av.isShowSequenceFeatures())
- {
- fr.transferSettings(ap.seqPanel.seqCanvas.fr);
- }
-
- resizing = true;
-
- if ((getSize().width > 0) && (getSize().height > 0))
- {
- od.setWidth(getSize().width);
- od.setHeight(getSize().height);
- }
- setSize(new Dimension(od.getWidth(), od.getHeight()));
-
- Thread thread = new Thread(this);
- thread.start();
- repaint();
- }
-
- @Override
- public void run()
- {
- miniMe = null;
-
- if (av.isShowSequenceFeatures())
- {
- fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
- }
-
- if (getSize().width > 0 && getSize().height > 0)
- {
- od.setWidth(getSize().width);
- od.setHeight(getSize().height);
- }
-
- setSize(new Dimension(od.getWidth(), od.getHeight()));
-
- miniMe = nullFrame.createImage(od.getWidth(), od.getHeight());
- offscreen = nullFrame.createImage(od.getWidth(), od.getHeight());
-
- Graphics mg = miniMe.getGraphics();
-<<<<<<< HEAD
-
- int alwidth = av.getAlignment().getWidth();
- int alheight = av.getAlignment().getAbsoluteHeight();
- float sampleCol = alwidth / (float) od.getWidth();
- float sampleRow = alheight / (float) od.getSequencesHeight();
-=======
- float sampleCol = (float) alwidth / (float) width;
- float sampleRow = (float) alheight / (float) sequencesHeight;
-
- int lastcol = 0, lastrow = 0;
- int xstart = 0, ystart = 0;
- Color color = Color.yellow;
- int row, col, sameRow = 0, sameCol = 0;
- jalview.datamodel.SequenceI seq;
- final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av
- .hasHiddenColumns();
- boolean hiddenRow = false;
- AlignmentI alignment = av.getAlignment();
-
- FeatureColourFinder finder = new FeatureColourFinder(fr);
- for (row = 0; row <= sequencesHeight; row++)
- {
- if (resizeAgain)
- {
- break;
- }
- if ((int) (row * sampleRow) == lastrow)
- {
- sameRow++;
- continue;
- }
-
- hiddenRow = false;
- if (hasHiddenRows)
- {
- seq = alignment.getHiddenSequences().getHiddenSequence(lastrow);
- if (seq == null)
- {
- int index = alignment.getHiddenSequences()
- .findIndexWithoutHiddenSeqs(lastrow);
-
- seq = alignment.getSequenceAt(index);
- }
- else
- {
- hiddenRow = true;
- }
- }
- else
- {
- seq = alignment.getSequenceAt(lastrow);
- }
-
- for (col = 0; col < width; col++)
- {
- if ((int) (col * sampleCol) == lastcol
- && (int) (row * sampleRow) == lastrow)
- {
- sameCol++;
- continue;
- }
-
- lastcol = (int) (col * sampleCol);
-
- if (seq.getLength() > lastcol)
- {
- color = sr.getResidueColour(seq, lastcol, finder);
- }
- else
- {
- color = Color.white;
- }
-
- if (hiddenRow
- || (hasHiddenCols && !av.getColumnSelection().isVisible(
- lastcol)))
- {
- color = color.darker().darker();
- }
-
- mg.setColor(color);
- if (sameCol == 1 && sameRow == 1)
- {
- mg.drawLine(xstart, ystart, xstart, ystart);
- }
- else
- {
- mg.fillRect(xstart, ystart, sameCol, sameRow);
- }
->>>>>>> bug/JAL-2436featureRendererThreading
-
- buildImage(sampleRow, sampleCol, mg);
-
- if (av.isShowAnnotation())
- {
- for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
- {
- mg.translate(col, od.getSequencesHeight());
- ap.annotationPanel.renderer.drawGraph(mg,
- av.getAlignmentConservationAnnotation(),
- av.getAlignmentConservationAnnotation().annotations,
- (int) (sampleCol) + 1, od.getGraphHeight(),
- (int) (col * sampleCol), (int) (col * sampleCol) + 1);
- mg.translate(-col, -od.getSequencesHeight());
- }
- }
- System.gc();
-
- resizing = false;
-
- setBoxPosition();
-
- if (resizeAgain)
- {
- resizeAgain = false;
- updateOverviewImage();
- }
- }
-
- /*
- * Build the overview panel image
- */
- private void buildImage(float sampleRow, float sampleCol, Graphics mg)
- {
- int lastcol = 0;
- int lastrow = 0;
- int xstart = 0;
- int ystart = 0;
- Color color = Color.yellow;
- int sameRow = 0;
- int sameCol = 0;
-
- SequenceI seq = null;
-
- final boolean hasHiddenCols = av.hasHiddenColumns();
- boolean hiddenRow = false;
-
- for (int row = 0; row <= od.getSequencesHeight() && !resizeAgain; row++)
- {
- if ((int) (row * sampleRow) == lastrow)
- {
- sameRow++;
- }
- else
- {
- // get the sequence which would be at alignment index 'lastrow' if no
- // columns were hidden, and determine whether it is hidden or not
- hiddenRow = av.getAlignment().isHidden(lastrow);
- seq = av.getAlignment().getSequenceAtAbsoluteIndex(lastrow);
-
- for (int col = 0; col < od.getWidth(); col++)
- {
- if ((int) (col * sampleCol) == lastcol
- && (int) (row * sampleRow) == lastrow)
- {
- sameCol++;
- }
- else
- {
- lastcol = (int) (col * sampleCol);
-
- color = getColumnColourFromSequence(seq, hiddenRow,
- hasHiddenCols, lastcol);
-
- mg.setColor(color);
- if (sameCol == 1 && sameRow == 1)
- {
- mg.drawLine(xstart, ystart, xstart, ystart);
- }
- else
- {
- mg.fillRect(xstart, ystart, sameCol, sameRow);
- }
-
- xstart = col;
- sameCol = 1;
- }
- }
- lastrow = (int) (row * sampleRow);
- ystart = row;
- sameRow = 1;
- }
- }
- }
-
- /*
- * Find the colour of a sequence at a specified column position
- */
- private Color getColumnColourFromSequence(
- jalview.datamodel.SequenceI seq, boolean hiddenRow,
- boolean hasHiddenCols, int lastcol)
- {
- Color color;
- if (seq.getLength() > lastcol)
- {
- color = sr.getResidueBoxColour(seq, lastcol);
-
- if (av.isShowSequenceFeatures())
- {
- color = fr.findFeatureColour(color, seq, lastcol);
- }
- }
- else
- {
- color = Color.white;
- }
-
- if (hiddenRow
- || (hasHiddenCols && !av.getColumnSelection()
- .isVisible(lastcol)))
- {
- color = color.darker().darker();
- }
- return color;
- }
-
- /**
- * Update the overview panel box when the associated alignment panel is
- * changed
- *
- */
- public void setBoxPosition()
- {
- od.setBoxPosition(av.getAlignment()
- .getHiddenSequences(), av.getColumnSelection(), av.getRanges());
- repaint();
- }
-
- @Override
- public void update(Graphics g)
- {
- paint(g);
- }
-
- @Override
- public void paint(Graphics g)
- {
- Graphics og = offscreen.getGraphics();
- if (miniMe != null)
- {
- og.drawImage(miniMe, 0, 0, this);
- og.setColor(Color.red);
- od.drawBox(og);
- g.drawImage(offscreen, 0, 0, this);
- }
- }
-
-}
+++ /dev/null
-package jalview.datamodel;
-
-
-/**
- * A profile for one column of an alignment
- *
- * @author gmcarstairs
- *
- */
-public class Profile implements ProfileI
-{
- /*
- * an object holding counts of symbols in the profile
- */
- private ResidueCount counts;
-
- /*
- * the number of sequences (gapped or not) in the profile
- */
- private int height;
-
- /*
- * the number of non-gapped sequences in the profile
- */
- private int gapped;
-
- /*
- * the highest count for any residue in the profile
- */
- private int maxCount;
-
- /*
- * the residue (e.g. K) or residues (e.g. KQW) with the
- * highest count in the profile
- */
- private String modalResidue;
-
- /**
- * Constructor which allows derived data to be stored without having to store
- * the full profile
- *
- * @param seqCount
- * the number of sequences in the profile
- * @param gaps
- * the number of gapped sequences
- * @param max
- * the highest count for any residue
- * @param modalres
- * the residue (or concatenated residues) with the highest count
- */
- public Profile(int seqCount, int gaps, int max, String modalRes)
- {
- this.height = seqCount;
- this.gapped = gaps;
- this.maxCount = max;
- this.modalResidue = modalRes;
- }
-
- /* (non-Javadoc)
- * @see jalview.datamodel.ProfileI#setCounts(jalview.datamodel.ResidueCount)
- */
- @Override
- public void setCounts(ResidueCount residueCounts)
- {
- this.counts = residueCounts;
- }
-
- /* (non-Javadoc)
- * @see jalview.datamodel.ProfileI#getPercentageIdentity(boolean)
- */
- @Override
- public float getPercentageIdentity(boolean ignoreGaps)
- {
- if (height == 0)
- {
- return 0f;
- }
- float pid = 0f;
- if (ignoreGaps && gapped < height)
- {
- pid = (maxCount * 100f) / (height - gapped);
- }
- else
- {
- pid = (maxCount * 100f) / height;
- }
- return pid;
- }
-
- /* (non-Javadoc)
- * @see jalview.datamodel.ProfileI#getCounts()
- */
- @Override
- public ResidueCount getCounts()
- {
- return counts;
- }
-
- /* (non-Javadoc)
- * @see jalview.datamodel.ProfileI#getHeight()
- */
- @Override
- public int getHeight()
- {
- return height;
- }
-
- /* (non-Javadoc)
- * @see jalview.datamodel.ProfileI#getGapped()
- */
- @Override
- public int getGapped()
- {
- return gapped;
- }
-
- /* (non-Javadoc)
- * @see jalview.datamodel.ProfileI#getMaxCount()
- */
- @Override
- public int getMaxCount()
- {
- return maxCount;
- }
-
- /* (non-Javadoc)
- * @see jalview.datamodel.ProfileI#getModalResidue()
- */
- @Override
- public String getModalResidue()
- {
- return modalResidue;
- }
-
- /* (non-Javadoc)
- * @see jalview.datamodel.ProfileI#getNonGapped()
- */
- @Override
- public int getNonGapped()
- {
- return height - gapped;
- }
-}
+++ /dev/null
-package jalview.datamodel;
-
-public interface ProfileI
-{
-
- /**
- * Set the full profile of counts
- *
- * @param residueCounts
- */
- public abstract void setCounts(ResidueCount residueCounts);
-
- /**
- * Returns the percentage identity of the profile, i.e. the highest proportion
- * of conserved (equal) symbols. The percentage is as a fraction of all
- * sequences, or only ungapped sequences if flag ignoreGaps is set true.
- *
- * @param ignoreGaps
- * @return
- */
- public abstract float getPercentageIdentity(boolean ignoreGaps);
-
- /**
- * Returns the full symbol counts for this profile
- *
- * @return
- */
- public abstract ResidueCount getCounts();
-
- /**
- * Returns the number of sequences in the profile
- *
- * @return
- */
- public abstract int getHeight();
-
- /**
- * Returns the number of sequences in the profile which had a gap character
- * (or were too short to be included in this column's profile)
- *
- * @return
- */
- public abstract int getGapped();
-
- /**
- * Returns the highest count for any symbol(s) in the profile
- *
- * @return
- */
- public abstract int getMaxCount();
-
- /**
- * Returns the symbol (or concatenated symbols) which have the highest count
- * in the profile, or an empty string if there were no symbols counted
- *
- * @return
- */
- public abstract String getModalResidue();
-
- /**
- * Answers the number of non-gapped sequences in the profile
- *
- * @return
- */
- public abstract int getNonGapped();
-
-}
\ No newline at end of file
+++ /dev/null
-package jalview.datamodel;
-
-public class Profiles implements ProfilesI
-{
-
- private ProfileI[] profiles;
-
- public Profiles(ProfileI[] p)
- {
- profiles = p;
- }
-
- /**
- * Returns the profile for the given column, or null if none found
- *
- * @param col
- */
- @Override
- public ProfileI get(int col)
- {
- return profiles != null && col >= 0 && col < profiles.length ? profiles[col]
- : null;
- }
-
- /**
- * Returns the first column (base 0) covered by the profiles
- */
- @Override
- public int getStartColumn()
- {
- return 0;
- }
-
- /**
- * Returns the last column (base 0) covered by the profiles
- */
- @Override
- public int getEndColumn()
- {
- return profiles == null ? 0 : profiles.length - 1;
- }
-
-}
+++ /dev/null
-package jalview.datamodel;
-
-public interface ProfilesI
-{
-
- ProfileI get(int i);
-
- int getStartColumn();
-
- int getEndColumn();
-
-}
+++ /dev/null
-package jalview.datamodel;
-
-import jalview.util.Comparison;
-import jalview.util.Format;
-import jalview.util.QuickSort;
-import jalview.util.SparseCount;
-
-/**
- * A class to count occurrences of residues in a profile, optimised for speed
- * and memory footprint.
- * @author gmcarstairs
- *
- */
-public class ResidueCount
-{
- /**
- * A data bean to hold the results of counting symbols
- */
- public class SymbolCounts
- {
- /**
- * the symbols seen (as char values), in no particular order
- */
- public final char[] symbols;
-
- /**
- * the counts for each symbol, in the same order as the symbols
- */
- public final int[] values;
-
- SymbolCounts(char[] s, int[] v)
- {
- symbols = s;
- values = v;
- }
- }
-
- private static final int TOUPPERCASE = 'A' - 'a';
-
- /*
- * nucleotide symbols to count (including N unknown)
- */
- private static final String NUCS = "ACGNTU";
-
- /*
- * amino acid symbols to count (including X unknown)
- * NB we also include U so as to support counting of RNA bases
- * in the "don't know" case of nucleotide / peptide
- */
- private static final String AAS = "ACDEFGHIKLMNPQRSTUVWXY";
-
- private static final int GAP_COUNT = 0;
-
- /*
- * fast lookup tables holding the index into our count
- * arrays of each symbol; index 0 is reserved for gap counting
- */
- private static int[] NUC_INDEX = new int[26];
-
- private static int[] AA_INDEX = new int[26];
- static
- {
- for (int i = 0; i < NUCS.length(); i++)
- {
- NUC_INDEX[NUCS.charAt(i) - 'A'] = i + 1;
- }
- for (int i = 0; i < AAS.length(); i++)
- {
- AA_INDEX[AAS.charAt(i) - 'A'] = i + 1;
- }
- }
-
- /*
- * counts array, just big enough for the nucleotide or peptide
- * character set (plus gap counts in position 0)
- */
- private short[] counts;
-
- /*
- * alternative array of int counts for use if any count
- * exceeds the maximum value of short (32767)
- */
- private int[] intCounts;
-
- /*
- * flag set if we switch from short to int counts
- */
- private boolean useIntCounts;
-
- /*
- * general-purpose counter, only for use for characters
- * that are not in the expected alphabet
- */
- private SparseCount otherData;
-
- /*
- * keeps track of the maximum count value recorded
- * (if this class ever allows decrements, would need to
- * calculate this on request instead)
- */
- int maxCount;
-
- /*
- * if we think we are counting nucleotide, can get by with smaller
- * array to hold counts
- */
- private boolean isNucleotide;
-
- /**
- * Default constructor allocates arrays able to count either nucleotide or
- * peptide bases. Use this constructor if not sure which the data is.
- */
- public ResidueCount()
- {
- this(false);
- }
-
- /**
- * Constructor that allocates an array just big enough for the anticipated
- * characters, plus one position to count gaps
- */
- public ResidueCount(boolean nucleotide)
- {
- isNucleotide = nucleotide;
- int charsToCount = nucleotide ? NUCS.length() : AAS.length();
- counts = new short[charsToCount + 1];
- }
-
- /**
- * Increments the count for the given character. The supplied character may be
- * upper or lower case but counts are for the upper case only. Gap characters
- * (space, ., -) are all counted together.
- *
- * @param c
- * @return the new value of the count for the character
- */
- public int add(final char c)
- {
- char u = toUpperCase(c);
- int newValue = 0;
- int offset = getOffset(u);
-
- /*
- * offset 0 is reserved for gap counting, so 0 here means either
- * an unexpected character, or a gap character passed in error
- */
- if (offset == 0)
- {
- if (Comparison.isGap(u))
- {
- newValue = addGap();
- }
- else
- {
- newValue = addOtherCharacter(u);
- }
- }
- else
- {
- newValue = increment(offset);
- }
- return newValue;
- }
-
- /**
- * Increment the count at the specified offset. If this would result in short
- * overflow, promote to counting int values instead.
- *
- * @param offset
- * @return the new value of the count at this offset
- */
- int increment(int offset)
- {
- int newValue = 0;
- if (useIntCounts)
- {
- newValue = intCounts[offset];
- intCounts[offset] = ++newValue;
- }
- else
- {
- if (counts[offset] == Short.MAX_VALUE)
- {
- handleOverflow();
- newValue = intCounts[offset];
- intCounts[offset] = ++newValue;
- }
- else
- {
- newValue = counts[offset];
- counts[offset] = (short) ++newValue;
- }
- }
- maxCount = Math.max(maxCount, newValue);
- return newValue;
- }
-
- /**
- * Switch from counting in short to counting in int
- */
- synchronized void handleOverflow()
- {
- intCounts = new int[counts.length];
- for (int i = 0; i < counts.length; i++)
- {
- intCounts[i] = counts[i];
- }
- counts = null;
- useIntCounts = true;
- }
-
- /**
- * Returns this character's offset in the count array
- *
- * @param c
- * @return
- */
- int getOffset(char c)
- {
- int offset = 0;
- if ('A' <= c && c <= 'Z')
- {
- offset = isNucleotide ? NUC_INDEX[c - 'A'] : AA_INDEX[c - 'A'];
- }
- return offset;
- }
-
- /**
- * @param c
- * @return
- */
- protected char toUpperCase(final char c)
- {
- char u = c;
- if ('a' <= c && c <= 'z')
- {
- u = (char) (c + TOUPPERCASE);
- }
- return u;
- }
-
- /**
- * Increment count for some unanticipated character. The first time this
- * called, a SparseCount is instantiated to hold these 'extra' counts.
- *
- * @param c
- * @return the new value of the count for the character
- */
- int addOtherCharacter(char c)
- {
- if (otherData == null)
- {
- otherData = new SparseCount();
- }
- int newValue = otherData.add(c, 1);
- maxCount = Math.max(maxCount, newValue);
- return newValue;
- }
-
- /**
- * Set count for some unanticipated character. The first time this called, a
- * SparseCount is instantiated to hold these 'extra' counts.
- *
- * @param c
- * @param value
- */
- void setOtherCharacter(char c, int value)
- {
- if (otherData == null)
- {
- otherData = new SparseCount();
- }
- otherData.put(c, value);
- }
-
- /**
- * Increment count of gap characters
- *
- * @return the new count of gaps
- */
- public int addGap()
- {
- int newValue;
- if (useIntCounts)
- {
- newValue = ++intCounts[GAP_COUNT];
- }
- else
- {
- newValue = ++counts[GAP_COUNT];
- }
- return newValue;
- }
-
- /**
- * Answers true if we are counting ints (only after overflow of short counts)
- *
- * @return
- */
- boolean isCountingInts()
- {
- return useIntCounts;
- }
-
- /**
- * Sets the count for the given character. The supplied character may be upper
- * or lower case but counts are for the upper case only.
- *
- * @param c
- * @param count
- */
- public void put(char c, int count)
- {
- char u = toUpperCase(c);
- int offset = getOffset(u);
-
- /*
- * offset 0 is reserved for gap counting, so 0 here means either
- * an unexpected character, or a gap character passed in error
- */
- if (offset == 0)
- {
- if (Comparison.isGap(u))
- {
- set(0, count);
- }
- else
- {
- setOtherCharacter(u, count);
- maxCount = Math.max(maxCount, count);
- }
- }
- else
- {
- set(offset, count);
- maxCount = Math.max(maxCount, count);
- }
- }
-
- /**
- * Sets the count at the specified offset. If this would result in short
- * overflow, promote to counting int values instead.
- *
- * @param offset
- * @param value
- */
- void set(int offset, int value)
- {
- if (useIntCounts)
- {
- intCounts[offset] = value;
- }
- else
- {
- if (value > Short.MAX_VALUE || value < Short.MIN_VALUE)
- {
- handleOverflow();
- intCounts[offset] = value;
- }
- else
- {
- counts[offset] = (short) value;
- }
- }
- }
-
- /**
- * Returns the count for the given character, or zero if no count held
- *
- * @param c
- * @return
- */
- public int getCount(char c)
- {
- char u = toUpperCase(c);
- int offset = getOffset(u);
- if (offset == 0)
- {
- if (!Comparison.isGap(u))
- {
- // should have called getGapCount()
- return otherData == null ? 0 : otherData.get(u);
- }
- }
- return useIntCounts ? intCounts[offset] : counts[offset];
- }
-
- public int getGapCount()
- {
- return useIntCounts ? intCounts[0] : counts[0];
- }
-
- /**
- * Answers true if this object wraps a counter for unexpected characters
- *
- * @return
- */
- boolean isUsingOtherData()
- {
- return otherData != null;
- }
-
- /**
- * Returns the character (or concatenated characters) for the symbol(s) with
- * the given count in the profile. Can be used to get the modal residue by
- * supplying the modal count value. Returns an empty string if no symbol has
- * the given count. The symbols are in alphabetic order of standard peptide or
- * nucleotide characters, followed by 'other' symbols if any.
- *
- * @return
- */
- public String getResiduesForCount(int count)
- {
- if (count == 0)
- {
- return "";
- }
-
- /*
- * find counts for the given value and append the
- * corresponding symbol
- */
- StringBuilder modal = new StringBuilder();
- if (useIntCounts)
- {
- for (int i = 1; i < intCounts.length; i++)
- {
- if (intCounts[i] == count)
- {
- modal.append(isNucleotide ? NUCS.charAt(i - 1) : AAS
- .charAt(i - 1));
- }
- }
- }
- else
- {
- for (int i = 1; i < counts.length; i++)
- {
- if (counts[i] == count)
- {
- modal.append(isNucleotide ? NUCS.charAt(i - 1) : AAS
- .charAt(i - 1));
- }
- }
- }
- if (otherData != null)
- {
- for (int i = 0; i < otherData.size(); i++)
- {
- if (otherData.valueAt(i) == count)
- {
- modal.append((char) otherData.keyAt(i));
- }
- }
- }
- return modal.toString();
- }
-
- /**
- * Returns the highest count for any symbol(s) in the profile (excluding gap)
- *
- * @return
- */
- public int getModalCount()
- {
- return maxCount;
- }
-
- /**
- * Returns the number of distinct symbols with a non-zero count (excluding the
- * gap symbol)
- *
- * @return
- */
- public int size() {
- int size = 0;
- if (useIntCounts)
- {
- for (int i = 1; i < intCounts.length; i++)
- {
- if (intCounts[i] > 0)
- {
- size++;
- }
- }
- }
- else
- {
- for (int i = 1; i < counts.length; i++)
- {
- if (counts[i] > 0)
- {
- size++;
- }
- }
- }
-
- /*
- * include 'other' characters recorded (even if count is zero
- * though that would be a strange use case)
- */
- if (otherData != null)
- {
- size += otherData.size();
- }
-
- return size;
- }
-
- /**
- * Returns a data bean holding those symbols that have a non-zero count
- * (excluding the gap symbol), with their counts.
- *
- * @return
- */
- public SymbolCounts getSymbolCounts()
- {
- int size = size();
- char[] symbols = new char[size];
- int[] values = new int[size];
- int j = 0;
-
- if (useIntCounts)
- {
- for (int i = 1; i < intCounts.length; i++)
- {
- if (intCounts[i] > 0)
- {
- char symbol = isNucleotide ? NUCS.charAt(i - 1) : AAS
- .charAt(i - 1);
- symbols[j] = symbol;
- values[j] = intCounts[i];
- j++;
- }
- }
- }
- else
- {
- for (int i = 1; i < counts.length; i++)
- {
- if (counts[i] > 0)
- {
- char symbol = isNucleotide ? NUCS.charAt(i - 1) : AAS
- .charAt(i - 1);
- symbols[j] = symbol;
- values[j] = counts[i];
- j++;
- }
- }
- }
- if (otherData != null)
- {
- for (int i = 0; i < otherData.size(); i++)
- {
- symbols[j] = (char) otherData.keyAt(i);
- values[j] = otherData.valueAt(i);
- j++;
- }
- }
-
- return new SymbolCounts(symbols, values);
- }
-
- /**
- * Returns a tooltip string showing residues in descending order of their
- * percentage frequency in the profile
- *
- * @param normaliseBy
- * the divisor for residue counts (may or may not include gapped
- * sequence count)
- * @param percentageDecPl
- * the number of decimal places to show in percentages
- * @return
- */
- public String getTooltip(int normaliseBy, int percentageDecPl)
- {
- SymbolCounts symbolCounts = getSymbolCounts();
- char[] ca = symbolCounts.symbols;
- int[] vl = symbolCounts.values;
-
- /*
- * sort characters into ascending order of their counts
- */
- QuickSort.sort(vl, ca);
-
- /*
- * traverse in reverse order (highest count first) to build tooltip
- */
- boolean first = true;
- StringBuilder sb = new StringBuilder(64);
- for (int c = ca.length - 1; c >= 0; c--)
- {
- final char residue = ca[c];
- // TODO combine residues which share a percentage
- // (see AAFrequency.completeCdnaConsensus)
- float tval = (vl[c] * 100f) / normaliseBy;
- sb.append(first ? "" : "; ").append(residue).append(" ");
- Format.appendPercentage(sb, tval, percentageDecPl);
- sb.append("%");
- first = false;
- }
- return sb.toString();
- }
-
- /**
- * Returns a string representation of the symbol counts, for debug purposes.
- */
- @Override
- public String toString()
- {
- StringBuilder sb = new StringBuilder();
- sb.append("[ ");
- SymbolCounts sc = getSymbolCounts();
- for (int i = 0; i < sc.symbols.length; i++)
- {
- sb.append(sc.symbols[i]).append(":").append(sc.values[i]).append(" ");
- }
- sb.append("]");
- return sb.toString();
- }
-}
+++ /dev/null
-package jalview.datamodel;
-
-/**
- * An interface that describes one matched region of an alignment, as one
- * contiguous portion of a single dataset sequence
- */
-public interface SearchResultMatchI
-{
- /**
- * Returns the matched sequence
- *
- * @return
- */
- SequenceI getSequence();
-
- /**
- * Returns the start position of the match in the sequence (base 1)
- *
- * @return
- */
- int getStart();
-
- /**
- * Returns the end position of the match in the sequence (base 1)
- *
- * @return
- */
- int getEnd();
-
-}
\ No newline at end of file
+++ /dev/null
-package jalview.datamodel;
-
-import java.util.BitSet;
-import java.util.List;
-
-/**
- * An interface describing the result of a search or other operation which
- * highlights matched regions of an alignment
- */
-public interface SearchResultsI
-{
-
- /**
- * Adds one region to the results
- *
- * @param seq
- * Sequence
- * @param start
- * int
- * @param end
- * int
- * @return
- */
- SearchResultMatchI addResult(SequenceI seq, int start, int end);
-
- /**
- * Answers true if the search results include the given sequence (or its
- * dataset sequence), else false
- *
- * @param sequence
- * @return
- */
- boolean involvesSequence(SequenceI sequence);
-
- /**
- * Returns an array of [from, to, from, to..] matched columns (base 0) between
- * the given start and end columns of the given sequence. Returns null if no
- * matches overlap the specified region.
- * <p>
- * Implementations should provide an optimised method to return locations to
- * highlight on a visible portion of an alignment.
- *
- * @param sequence
- * @param start
- * first column of range (base 0, inclusive)
- * @param end
- * last column of range base 0, inclusive)
- * @return int[]
- */
- int[] getResults(SequenceI sequence, int start, int end);
-
- /**
- * Returns the number of matches found
- *
- * @return
- */
- int getSize();
-
- /**
- * Returns true if no search result matches are held.
- *
- * @return
- */
- boolean isEmpty();
-
- /**
- * Returns the list of matches.
- *
- * @return
- */
- List<SearchResultMatchI> getResults();
-
- /**
- * Set bits in a bitfield for all columns in the given sequence collection
- * that are highlighted
- *
- * @param sqcol
- * the set of sequences to search for highlighted regions
- * @param bs
- * bitset to set
- * @return number of bits set
- */
- int markColumns(SequenceCollectionI sqcol, BitSet bs);
-}
\ No newline at end of file
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.ext.jmol;
-
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.io.FileParse;
-import jalview.io.StructureFile;
-import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureImportSettings;
-import jalview.util.Format;
-import jalview.util.MessageManager;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Vector;
-
-import javajs.awt.Dimension;
-
-import org.jmol.api.JmolStatusListener;
-import org.jmol.api.JmolViewer;
-import org.jmol.c.CBK;
-import org.jmol.c.STR;
-import org.jmol.modelset.ModelSet;
-import org.jmol.viewer.Viewer;
-
-import MCview.Atom;
-import MCview.PDBChain;
-import MCview.Residue;
-
-/**
- * Import and process files with Jmol for file like PDB, mmCIF
- *
- * @author jprocter
- *
- */
-public class JmolParser extends StructureFile implements JmolStatusListener
-{
- Viewer viewer = null;
-
- public JmolParser(String inFile, String type) throws IOException
- {
- super(inFile, type);
- }
-
- public JmolParser(FileParse fp) throws IOException
- {
- super(fp);
- }
-
- public JmolParser()
- {
- }
-
- /**
- * Calls the Jmol library to parse the PDB/mmCIF file, and then inspects the
- * resulting object model to generate Jalview-style sequences, with secondary
- * structure annotation added where available (i.e. where it has been computed
- * by Jmol using DSSP).
- *
- * @see jalview.io.AlignFile#parse()
- */
- @Override
- public void parse() throws IOException
- {
- setChains(new Vector<PDBChain>());
- Viewer jmolModel = getJmolData();
- jmolModel.openReader(getDataName(), getDataName(), getReader());
- waitForScript(jmolModel);
-
- /*
- * Convert one or more Jmol Model objects to Jalview sequences
- */
- if (jmolModel.ms.mc > 0)
- {
- // ideally we do this
- // try
- // {
- // setStructureFileType(jmolModel.evalString("show _fileType"));
- // } catch (Exception q)
- // {
- // }
- // ;
- // instead, we distinguish .cif from non-.cif by filename
- setStructureFileType(getDataName().toLowerCase().endsWith(".cif") ? PDBEntry.Type.MMCIF
- .toString() : "PDB");
-
- transformJmolModelToJalview(jmolModel.ms);
- }
- }
-
- /**
- * create a headless jmol instance for dataprocessing
- *
- * @return
- */
- private Viewer getJmolData()
- {
- if (viewer == null)
- {
- try
- {
- /*
- * params -o (output to sysout) -n (nodisplay) -x (exit when finished)
- * see http://wiki.jmol.org/index.php/Jmol_Application
- */
- viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null,
- null, "-x -o -n", this);
- // ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used
- viewer.setBooleanProperty("defaultStructureDSSP", true);
- } catch (ClassCastException x)
- {
- throw new Error(MessageManager.formatMessage(
- "error.jmol_version_not_compatible_with_jalview_version",
- new String[] { JmolViewer.getJmolVersion() }), x);
- }
- }
- return viewer;
- }
-
- public void transformJmolModelToJalview(ModelSet ms) throws IOException
- {
- try
- {
- String lastID = "";
- List<SequenceI> rna = new ArrayList<SequenceI>();
- List<SequenceI> prot = new ArrayList<SequenceI>();
- PDBChain tmpchain;
- String pdbId = (String) ms.getInfo(0, "title");
-
- if (pdbId == null)
- {
- setId(safeName(getDataName()));
- setPDBIdAvailable(false);
- }
- else
- {
- setId(pdbId);
- setPDBIdAvailable(true);
- }
- List<Atom> significantAtoms = convertSignificantAtoms(ms);
- for (Atom tmpatom : significantAtoms)
- {
- try
- {
- tmpchain = findChain(tmpatom.chain);
- if (tmpatom.resNumIns.trim().equals(lastID))
- {
- // phosphorylated protein - seen both CA and P..
- continue;
- }
- tmpchain.atoms.addElement(tmpatom);
- } catch (Exception e)
- {
- tmpchain = new PDBChain(getId(), tmpatom.chain);
- getChains().add(tmpchain);
- tmpchain.atoms.addElement(tmpatom);
- }
- lastID = tmpatom.resNumIns.trim();
- }
- xferSettings();
-
- makeResidueList();
- makeCaBondList();
-
-<<<<<<< HEAD
-=======
- if (getId() == null)
- {
- // always use resource name, not the hardwired file
- // Does the value of ID get used ? Behaviour needs to be
- // documented and tested
- setId(getDataName());
- }
->>>>>>> spike/JAL-2040_JAL-2137_phyre2
- for (PDBChain chain : getChains())
- {
- SequenceI chainseq = postProcessChain(chain);
- if (isRNA(chainseq))
- {
- rna.add(chainseq);
- }
- else
- {
- prot.add(chainseq);
- }
-
- if (StructureImportSettings.isProcessSecondaryStructure())
- {
- createAnnotation(chainseq, chain, ms.at);
- }
- }
- } catch (OutOfMemoryError er)
- {
- System.out
- .println("OUT OF MEMORY LOADING TRANSFORMING JMOL MODEL TO JALVIEW MODEL");
- throw new IOException(
- MessageManager
- .getString("exception.outofmemory_loading_mmcif_file"));
- }
- }
-
- private List<Atom> convertSignificantAtoms(ModelSet ms)
- {
- List<Atom> significantAtoms = new ArrayList<Atom>();
- HashMap<String, org.jmol.modelset.Atom> chainTerMap = new HashMap<String, org.jmol.modelset.Atom>();
- org.jmol.modelset.Atom prevAtom = null;
- for (org.jmol.modelset.Atom atom : ms.at)
- {
- if (atom.getAtomName().equalsIgnoreCase("CA")
- || atom.getAtomName().equalsIgnoreCase("P"))
- {
- if (!atomValidated(atom, prevAtom, chainTerMap))
- {
- continue;
- }
- Atom curAtom = new Atom(atom.x, atom.y, atom.z);
- curAtom.atomIndex = atom.getIndex();
- curAtom.chain = atom.getChainIDStr();
- curAtom.insCode = atom.group.getInsertionCode() == '\000' ? ' '
- : atom.group.getInsertionCode();
- curAtom.name = atom.getAtomName();
- curAtom.number = atom.getAtomNumber();
- curAtom.resName = atom.getGroup3(true);
- curAtom.resNumber = atom.getResno();
- curAtom.occupancy = ms.occupancies != null ? ms.occupancies[atom
- .getIndex()] : Float.valueOf(atom.getOccupancy100());
- String fmt = new Format("%4i").form(curAtom.resNumber);
- curAtom.resNumIns = (fmt + curAtom.insCode);
- curAtom.tfactor = atom.getBfactor100() / 100f;
- curAtom.type = 0;
- // significantAtoms.add(curAtom);
- // ignore atoms from subsequent models
- if (!significantAtoms.contains(curAtom))
- {
- significantAtoms.add(curAtom);
- }
- prevAtom = atom;
- }
- }
- return significantAtoms;
- }
-
- private boolean atomValidated(org.jmol.modelset.Atom curAtom,
- org.jmol.modelset.Atom prevAtom,
- HashMap<String, org.jmol.modelset.Atom> chainTerMap)
- {
- // System.out.println("Atom: " + curAtom.getAtomNumber()
- // + " Last atom index " + curAtom.group.lastAtomIndex);
- if (chainTerMap == null || prevAtom == null)
- {
- return true;
- }
- String curAtomChId = curAtom.getChainIDStr();
- String prevAtomChId = prevAtom.getChainIDStr();
- // new chain encoutered
- if (!prevAtomChId.equals(curAtomChId))
- {
- // On chain switch add previous chain termination to xTerMap if not exists
- if (!chainTerMap.containsKey(prevAtomChId))
- {
- chainTerMap.put(prevAtomChId, prevAtom);
- }
- // if current atom belongs to an already terminated chain and the resNum
- // diff < 5 then mark as valid and update termination Atom
- if (chainTerMap.containsKey(curAtomChId))
- {
- if (curAtom.getResno() < chainTerMap.get(curAtomChId).getResno())
- {
- return false;
- }
- if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
- {
- chainTerMap.put(curAtomChId, curAtom);
- return true;
- }
- return false;
- }
- }
- // atom with previously terminated chain encountered
- else if (chainTerMap.containsKey(curAtomChId))
- {
- if (curAtom.getResno() < chainTerMap.get(curAtomChId).getResno())
- {
- return false;
- }
- if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
- {
- chainTerMap.put(curAtomChId, curAtom);
- return true;
- }
- return false;
- }
- // HETATM with resNum jump > 2
- return !(curAtom.isHetero() && ((curAtom.getResno() - prevAtom
- .getResno()) > 2));
- }
-
- private void createAnnotation(SequenceI sequence, PDBChain chain,
- org.jmol.modelset.Atom[] jmolAtoms)
- {
- char[] secstr = new char[sequence.getLength()];
- char[] secstrcode = new char[sequence.getLength()];
-
- // Ensure Residue size equals Seq size
- if (chain.residues.size() != sequence.getLength())
- {
- return;
- }
- int annotIndex = 0;
- for (Residue residue : chain.residues)
- {
- Atom repAtom = residue.getAtoms().get(0);
- STR proteinStructureSubType = jmolAtoms[repAtom.atomIndex].group
- .getProteinStructureSubType();
- setSecondaryStructure(proteinStructureSubType, annotIndex, secstr,
- secstrcode);
- ++annotIndex;
- }
- addSecondaryStructureAnnotation(chain.pdbid, sequence, secstr,
- secstrcode, chain.id, sequence.getStart());
- }
-
- /**
- * Helper method that adds an AlignmentAnnotation for secondary structure to
- * the sequence, provided at least one secondary structure prediction has been
- * made
- *
- * @param modelTitle
- * @param seq
- * @param secstr
- * @param secstrcode
- * @param chainId
- * @param firstResNum
- * @return
- */
- protected void addSecondaryStructureAnnotation(String modelTitle,
- SequenceI sq, char[] secstr, char[] secstrcode, String chainId,
- int firstResNum)
- {
- char[] seq = sq.getSequence();
- boolean ssFound = false;
- Annotation asecstr[] = new Annotation[seq.length + firstResNum - 1];
- for (int p = 0; p < seq.length; p++)
- {
- if (secstr[p] >= 'A' && secstr[p] <= 'z')
- {
- try
- {
- asecstr[p] = new Annotation(String.valueOf(secstr[p]), null,
- secstrcode[p], Float.NaN);
- ssFound = true;
- } catch (Exception e)
- {
- // e.printStackTrace();
- }
- }
- }
-
- if (ssFound)
- {
- String mt = modelTitle == null ? getDataName() : modelTitle;
- mt += chainId;
- AlignmentAnnotation ann = new AlignmentAnnotation(
- "Secondary Structure", "Secondary Structure for " + mt,
- asecstr);
- ann.belowAlignment = true;
- ann.visible = true;
- ann.autoCalculated = false;
- ann.setCalcId(getClass().getName());
- ann.adjustForAlignment();
- ann.validateRangeAndDisplay();
- annotations.add(ann);
- sq.addAlignmentAnnotation(ann);
- }
- }
-
- private void waitForScript(Viewer jmd)
- {
- while (jmd.isScriptExecuting())
- {
- try
- {
- Thread.sleep(50);
-
- } catch (InterruptedException x)
- {
- }
- }
- }
-
- /**
- * Convert Jmol's secondary structure code to Jalview's, and stored it in the
- * secondary structure arrays at the given sequence position
- *
- * @param proteinStructureSubType
- * @param pos
- * @param secstr
- * @param secstrcode
- */
- protected void setSecondaryStructure(STR proteinStructureSubType,
- int pos, char[] secstr, char[] secstrcode)
- {
- switch (proteinStructureSubType)
- {
- case HELIX310:
- secstr[pos] = '3';
- break;
- case HELIX:
- case HELIXALPHA:
- secstr[pos] = 'H';
- break;
- case HELIXPI:
- secstr[pos] = 'P';
- break;
- case SHEET:
- secstr[pos] = 'E';
- break;
- default:
- secstr[pos] = 0;
- }
-
- switch (proteinStructureSubType)
- {
- case HELIX310:
- case HELIXALPHA:
- case HELIXPI:
- case HELIX:
- secstrcode[pos] = 'H';
- break;
- case SHEET:
- secstrcode[pos] = 'E';
- break;
- default:
- secstrcode[pos] = 0;
- }
- }
-
- /**
- * Convert any non-standard peptide codes to their standard code table
- * equivalent. (Initial version only does Selenomethionine MSE->MET.)
- *
- * @param threeLetterCode
- * @param seq
- * @param pos
- */
- protected void replaceNonCanonicalResidue(String threeLetterCode,
- char[] seq, int pos)
- {
- String canonical = ResidueProperties
- .getCanonicalAminoAcid(threeLetterCode);
- if (canonical != null && !canonical.equalsIgnoreCase(threeLetterCode))
- {
- seq[pos] = ResidueProperties.getSingleCharacterCode(canonical);
- }
- }
-
- /**
- * Not implemented - returns null
- */
- @Override
- public String print()
- {
- return null;
- }
-
- /**
- * Not implemented
- */
- @Override
- public void setCallbackFunction(String callbackType,
- String callbackFunction)
- {
- }
-
- @Override
- public void notifyCallback(CBK cbType, Object[] data)
- {
- String strInfo = (data == null || data[1] == null ? null : data[1]
- .toString());
- switch (cbType)
- {
- case ECHO:
- sendConsoleEcho(strInfo);
- break;
- case SCRIPT:
- notifyScriptTermination((String) data[2],
- ((Integer) data[3]).intValue());
- break;
- case MEASURE:
- String mystatus = (String) data[3];
- if (mystatus.indexOf("Picked") >= 0
- || mystatus.indexOf("Sequence") >= 0)
- {
- // Picking mode
- sendConsoleMessage(strInfo);
- }
- else if (mystatus.indexOf("Completed") >= 0)
- {
- sendConsoleEcho(strInfo.substring(strInfo.lastIndexOf(",") + 2,
- strInfo.length() - 1));
- }
- break;
- case MESSAGE:
- sendConsoleMessage(data == null ? null : strInfo);
- break;
- case PICK:
- sendConsoleMessage(strInfo);
- break;
- default:
- break;
- }
- }
-
- String lastConsoleEcho = "";
-
- private void sendConsoleEcho(String string)
- {
- lastConsoleEcho += string;
- lastConsoleEcho += "\n";
- }
-
- String lastConsoleMessage = "";
-
- private void sendConsoleMessage(String string)
- {
- lastConsoleMessage += string;
- lastConsoleMessage += "\n";
- }
-
- int lastScriptTermination = -1;
-
- String lastScriptMessage = "";
-
- private void notifyScriptTermination(String string, int intValue)
- {
- lastScriptMessage += string;
- lastScriptMessage += "\n";
- lastScriptTermination = intValue;
- }
-
- @Override
- public boolean notifyEnabled(CBK callbackPick)
- {
- switch (callbackPick)
- {
- case MESSAGE:
- case SCRIPT:
- case ECHO:
- case LOADSTRUCT:
- case ERROR:
- return true;
- default:
- return false;
- }
- }
-
- /**
- * Not implemented - returns null
- */
- @Override
- public String eval(String strEval)
- {
- return null;
- }
-
- /**
- * Not implemented - returns null
- */
- @Override
- public float[][] functionXY(String functionName, int x, int y)
- {
- return null;
- }
-
- /**
- * Not implemented - returns null
- */
- @Override
- public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
- {
- return null;
- }
-
- /**
- * Not implemented - returns null
- */
- @Override
- public String createImage(String fileName, String imageType,
- Object text_or_bytes, int quality)
- {
- return null;
- }
-
- /**
- * Not implemented - returns null
- */
- @Override
- public Map<String, Object> getRegistryInfo()
- {
- return null;
- }
-
- /**
- * Not implemented
- */
- @Override
- public void showUrl(String url)
- {
- }
-
- /**
- * Not implemented - returns null
- */
- @Override
- public Dimension resizeInnerPanel(String data)
- {
- return null;
- }
-
- @Override
- public Map<String, Object> getJSpecViewProperty(String arg0)
- {
- return null;
- }
-
- public boolean isPredictSecondaryStructure()
- {
- return predictSecondaryStructure;
- }
-
- public void setPredictSecondaryStructure(boolean predictSecondaryStructure)
- {
- this.predictSecondaryStructure = predictSecondaryStructure;
- }
-
- public boolean isVisibleChainAnnotation()
- {
- return visibleChainAnnotation;
- }
-
- public void setVisibleChainAnnotation(boolean visibleChainAnnotation)
- {
- this.visibleChainAnnotation = visibleChainAnnotation;
- }
-
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.gui;
-
-import jalview.datamodel.SequenceI;
-import jalview.renderer.AnnotationRenderer;
-import jalview.viewmodel.OverviewDimensions;
-import jalview.renderer.seqfeatures.FeatureColourFinder;
-
-import java.awt.Color;
-import java.awt.Dimension;
-import java.awt.Graphics;
-import java.awt.event.ComponentAdapter;
-import java.awt.event.ComponentEvent;
-import java.awt.event.MouseAdapter;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseMotionAdapter;
-import java.awt.image.BufferedImage;
-
-import javax.swing.JPanel;
-
-/**
- * Panel displaying an overview of the full alignment, with an interactive box
- * representing the viewport onto the alignment.
- *
- * @author $author$
- * @version $Revision$
- */
-public class OverviewPanel extends JPanel implements Runnable
-{
- private static final Color TRANS_GREY = new Color(100, 100, 100, 25);
-
- private final AnnotationRenderer renderer = new AnnotationRenderer();
-
- private OverviewDimensions od;
-
- private BufferedImage miniMe;
-
- private BufferedImage lastMiniMe = null;
-
- private AlignViewport av;
-
- private AlignmentPanel ap;
-
- //
- private boolean resizing = false;
-
- // This is set true if the user resizes whilst
- // the overview is being calculated
- private boolean resizeAgain = false;
-
- // Can set different properties in this seqCanvas than
- // main visible SeqCanvas
- private SequenceRenderer sr;
-
- private jalview.renderer.seqfeatures.FeatureRenderer fr;
-
- /**
- * Creates a new OverviewPanel object.
- *
- * @param alPanel
- * The alignment panel which is shown in the overview panel
- */
- public OverviewPanel(AlignmentPanel alPanel)
- {
- this.av = alPanel.av;
- this.ap = alPanel;
- setLayout(null);
-
- sr = new SequenceRenderer(av);
- sr.renderGaps = false;
- sr.forOverview = true;
- fr = new FeatureRenderer(alPanel);
-
- od = new OverviewDimensions(av.getRanges(), av.isShowAnnotation());
-
- addComponentListener(new ComponentAdapter()
- {
- @Override
- public void componentResized(ComponentEvent evt)
- {
- if ((getWidth() != od.getWidth())
- || (getHeight() != (od.getHeight())))
- {
- updateOverviewImage();
- }
- }
- });
-
- addMouseMotionListener(new MouseMotionAdapter()
- {
- @Override
- public void mouseDragged(MouseEvent evt)
- {
- if (!av.getWrapAlignment())
- {
- od.updateViewportFromMouse(evt.getX(), evt.getY(), av
- .getAlignment().getHiddenSequences(), av
- .getColumnSelection(), av.getRanges());
- ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
- }
- }
- });
-
- addMouseListener(new MouseAdapter()
- {
- @Override
- public void mousePressed(MouseEvent evt)
- {
- if (!av.getWrapAlignment())
- {
- od.updateViewportFromMouse(evt.getX(), evt.getY(), av
- .getAlignment().getHiddenSequences(), av
- .getColumnSelection(), av.getRanges());
- ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
- }
- }
- });
-
- updateOverviewImage();
- }
-
- /**
- * Updates the overview image when the related alignment panel is updated
- */
- public void updateOverviewImage()
- {
- if (resizing)
- {
- resizeAgain = true;
- return;
- }
-
- resizing = true;
-
- if ((getWidth() > 0) && (getHeight() > 0))
- {
- od.setWidth(getWidth());
- od.setHeight(getHeight());
- }
-
- setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
-
- Thread thread = new Thread(this);
- thread.start();
- repaint();
- }
-
- @Override
- public void run()
- {
- miniMe = null;
-
- if (av.isShowSequenceFeatures())
- {
- fr.transferSettings(ap.getSeqPanel().seqCanvas.getFeatureRenderer());
- }
-
- // why do we need to set preferred size again? was set in
- // updateOverviewImage
- setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
-
- miniMe = new BufferedImage(od.getWidth(), od.getHeight(),
- BufferedImage.TYPE_INT_RGB);
-
- Graphics mg = miniMe.getGraphics();
- mg.setColor(Color.orange);
- mg.fillRect(0, 0, od.getWidth(), miniMe.getHeight());
-
-<<<<<<< HEAD
- // calculate sampleCol and sampleRow
- // alignment width is max number of residues/bases
- // alignment height is number of sequences
- int alwidth = av.getAlignment().getWidth();
- int alheight = av.getAlignment().getAbsoluteHeight();
-
- // sampleCol or sampleRow is the width/height allocated to each residue
- // in particular, sometimes we may need more than one row/col of the
- // BufferedImage allocated
- // sampleCol is how much of a residue to assign to each pixel
- // sampleRow is how many sequences to assign to each pixel
- float sampleCol = alwidth / (float) od.getWidth();
- float sampleRow = alheight / (float) od.getSequencesHeight();
-
- buildImage(sampleRow, sampleCol);
-=======
- float sampleCol = (float) alwidth / (float) width;
- float sampleRow = (float) alheight / (float) sequencesHeight;
-
- int lastcol = -1, lastrow = -1;
- Color color = Color.white;
- int row, col;
- jalview.datamodel.SequenceI seq;
- final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av
- .hasHiddenColumns();
- boolean hiddenRow = false;
- // get hidden row and hidden column map once at beginning.
- // clone featureRenderer settings to avoid race conditions... if state is
- // updated just need to refresh again
-
- FeatureColourFinder finder = new FeatureColourFinder(fr);
-
- for (row = 0; row < sequencesHeight; row++)
- {
- if (resizeAgain)
- {
- break;
- }
- if ((int) (row * sampleRow) == lastrow)
- {
- // No need to recalculate the colours,
- // Just copy from the row above
- for (col = 0; col < width; col++)
- {
- if (resizeAgain)
- {
- break;
- }
- miniMe.setRGB(col, row, miniMe.getRGB(col, row - 1));
- }
- continue;
- }
-
- lastrow = (int) (row * sampleRow);
-
- hiddenRow = false;
- if (hasHiddenRows)
- {
- seq = av.getAlignment().getHiddenSequences()
- .getHiddenSequence(lastrow);
- if (seq == null)
- {
- int index = av.getAlignment().getHiddenSequences()
- .findIndexWithoutHiddenSeqs(lastrow);
-
- seq = av.getAlignment().getSequenceAt(index);
- }
- else
- {
- hiddenRow = true;
- }
- }
- else
- {
- seq = av.getAlignment().getSequenceAt(lastrow);
- }
-
- if (seq == null)
- {
- System.out.println(lastrow + " null");
- continue;
- }
-
- for (col = 0; col < width; col++)
- {
- if (resizeAgain)
- {
- break;
- }
- if ((int) (col * sampleCol) == lastcol
- && (int) (row * sampleRow) == lastrow)
- {
- miniMe.setRGB(col, row, color.getRGB());
- continue;
- }
-
- lastcol = (int) (col * sampleCol);
-
- if (seq.getLength() > lastcol)
- {
- color = sr.getResidueColour(seq, lastcol, finder);
- }
- else
- {
- color = Color.WHITE;
- }
-
- if (hiddenRow
- || (hasHiddenCols && !av.getColumnSelection().isVisible(
- lastcol)))
- {
- color = color.darker().darker();
- }
-
- miniMe.setRGB(col, row, color.getRGB());
->>>>>>> bug/JAL-2436featureRendererThreading
-
- if (av.isShowAnnotation())
- {
- renderer.updateFromAlignViewport(av);
- for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
- {
- mg.translate(col, od.getSequencesHeight());
- renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),
- av.getAlignmentConservationAnnotation().annotations,
- (int) (sampleCol) + 1, od.getGraphHeight(),
- (int) (col * sampleCol), (int) (col * sampleCol) + 1);
- mg.translate(-col, -od.getSequencesHeight());
-
- }
- }
- System.gc();
-
- resizing = false;
-
- if (resizeAgain)
- {
- resizeAgain = false;
- updateOverviewImage();
- }
- else
- {
- lastMiniMe = miniMe;
- }
-
- setBoxPosition();
- }
-
- /*
- * Build the overview panel image
- */
- private void buildImage(float sampleRow, float sampleCol)
- {
- int lastcol = -1;
- int lastrow = -1;
- int color = Color.white.getRGB();
-
- SequenceI seq = null;
-
- final boolean hasHiddenCols = av.hasHiddenColumns();
- boolean hiddenRow = false;
- // get hidden row and hidden column map once at beginning.
- // clone featureRenderer settings to avoid race conditions... if state is
- // updated just need to refresh again
- for (int row = 0; row < od.getSequencesHeight() && !resizeAgain; row++)
- {
- boolean doCopy = true;
- int currentrow = (int) (row * sampleRow);
- if (currentrow != lastrow)
- {
- doCopy = false;
-
- lastrow = currentrow;
-
- // get the sequence which would be at alignment index 'lastrow' if no
- // rows were hidden, and determine whether it is hidden or not
- hiddenRow = av.getAlignment().isHidden(lastrow);
- seq = av.getAlignment().getSequenceAtAbsoluteIndex(lastrow);
- }
-
- for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
- {
- if (doCopy)
- {
- color = miniMe.getRGB(col, row - 1);
- }
- else if ((int) (col * sampleCol) != lastcol
- || (int) (row * sampleRow) != lastrow)
- {
- lastcol = (int) (col * sampleCol);
- color = getColumnColourFromSequence(seq, hiddenRow, hasHiddenCols,
- lastcol);
- }
- // else we just use the color we already have , so don't need to set it
-
- miniMe.setRGB(col, row, color);
- }
- }
- }
-
- /*
- * Find the colour of a sequence at a specified column position
- */
- private int getColumnColourFromSequence(jalview.datamodel.SequenceI seq,
- boolean hiddenRow, boolean hasHiddenCols, int lastcol)
- {
- int color;
-
- if (seq == null)
- {
- color = Color.white.getRGB();
- }
- else if (seq.getLength() > lastcol)
- {
- color = sr.getResidueBoxColour(seq, lastcol).getRGB();
-
- if (av.isShowSequenceFeatures())
- {
- color = fr.findFeatureColour(color, seq, lastcol);
- }
- }
- else
- {
- color = Color.white.getRGB();
- }
-
- if (hiddenRow
- || (hasHiddenCols && !av.getColumnSelection()
- .isVisible(lastcol)))
- {
- color = new Color(color).darker().darker().getRGB();
- }
-
- return color;
- }
-
- /**
- * Update the overview panel box when the associated alignment panel is
- * changed
- *
- */
- public void setBoxPosition()
- {
- od.setBoxPosition(av.getAlignment()
- .getHiddenSequences(), av.getColumnSelection(), av.getRanges());
- repaint();
- }
-
-
- @Override
- public void paintComponent(Graphics g)
- {
- if (resizing || resizeAgain)
- {
- if (lastMiniMe == null)
- {
- g.setColor(Color.white);
- g.fillRect(0, 0, getWidth(), getHeight());
- }
- else
- {
- g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
- }
- g.setColor(TRANS_GREY);
- g.fillRect(0, 0, getWidth(), getHeight());
- }
- else if (lastMiniMe != null)
- {
- g.drawImage(lastMiniMe, 0, 0, this);
- if (lastMiniMe != miniMe)
- {
- g.setColor(TRANS_GREY);
- g.fillRect(0, 0, getWidth(), getHeight());
- }
- }
-
- g.setColor(Color.red);
- od.drawBox(g);
- }
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-
-package jalview.gui;
-
-import jalview.bin.Jalview;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.fts.api.FTSData;
-import jalview.fts.api.FTSDataColumnI;
-import jalview.fts.api.FTSRestClientI;
-import jalview.fts.core.FTSRestRequest;
-import jalview.fts.core.FTSRestResponse;
-import jalview.fts.service.pdb.PDBFTSRestClient;
-import jalview.jbgui.GStructureChooser;
-import jalview.structure.StructureSelectionManager;
-import jalview.util.MessageManager;
-import jalview.ws.DBRefFetcher;
-import jalview.ws.sifts.SiftsSettings;
-
-import java.awt.event.ItemEvent;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.LinkedHashSet;
-import java.util.List;
-import java.util.Objects;
-import java.util.Vector;
-
-import javax.swing.JCheckBox;
-import javax.swing.JComboBox;
-import javax.swing.JLabel;
-import javax.swing.JOptionPane;
-import javax.swing.table.AbstractTableModel;
-
-/**
- * Provides the behaviors for the Structure chooser Panel
- *
- * @author tcnofoegbu
- *
- */
-@SuppressWarnings("serial")
-public class StructureChooser extends GStructureChooser implements
- IProgressIndicator
-{
- private boolean structuresDiscovered = false;
-
- private SequenceI selectedSequence;
-
- private SequenceI[] selectedSequences;
-
- private IProgressIndicator progressIndicator;
-
- private Collection<FTSData> discoveredStructuresSet;
-
- private FTSRestRequest lastPdbRequest;
-
- private FTSRestClientI pdbRestCleint;
-
- private String selectedPdbFileName;
-
- private boolean isValidPBDEntry;
-
- public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
- AlignmentPanel ap)
- {
- this.ap = ap;
- this.selectedSequence = selectedSeq;
- this.selectedSequences = selectedSeqs;
- this.progressIndicator = (ap == null) ? null : ap.alignFrame;
- init();
- }
-
- /**
- * Initializes parameters used by the Structure Chooser Panel
- */
- public void init()
- {
- if (!Jalview.isHeadlessMode())
- {
- progressBar = new ProgressBar(this.statusPanel, this.statusBar);
- }
-
- Thread discoverPDBStructuresThread = new Thread(new Runnable()
- {
- @Override
- public void run()
- {
- long startTime = System.currentTimeMillis();
- updateProgressIndicator(MessageManager
- .getString("status.loading_cached_pdb_entries"), startTime);
- loadLocalCachedPDBEntries();
- updateProgressIndicator(null, startTime);
- updateProgressIndicator(MessageManager
- .getString("status.searching_for_pdb_structures"),
- startTime);
- fetchStructuresMetaData();
- populateFilterComboBox();
- updateProgressIndicator(null, startTime);
- mainFrame.setVisible(true);
- updateCurrentView();
- }
- });
- discoverPDBStructuresThread.start();
- }
-
- /**
- * Updates the progress indicator with the specified message
- *
- * @param message
- * displayed message for the operation
- * @param id
- * unique handle for this indicator
- */
- public void updateProgressIndicator(String message, long id)
- {
- if (progressIndicator != null)
- {
- progressIndicator.setProgressBar(message, id);
- }
- }
-
- /**
- * Retrieve meta-data for all the structure(s) for a given sequence(s) in a
- * selection group
- */
- public void fetchStructuresMetaData()
- {
- long startTime = System.currentTimeMillis();
- pdbRestCleint = PDBFTSRestClient.getInstance();
- Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
- .getStructureSummaryFields();
-
- discoveredStructuresSet = new LinkedHashSet<FTSData>();
- HashSet<String> errors = new HashSet<String>();
- for (SequenceI seq : selectedSequences)
- {
- FTSRestRequest pdbRequest = new FTSRestRequest();
- pdbRequest.setAllowEmptySeq(false);
- pdbRequest.setResponseSize(500);
- pdbRequest.setFieldToSearchBy("(");
- pdbRequest.setWantedFields(wantedFields);
- pdbRequest.setSearchTerm(buildQuery(seq) + ")");
- pdbRequest.setAssociatedSequence(seq);
- FTSRestResponse resultList;
- try
- {
- resultList = pdbRestCleint.executeRequest(pdbRequest);
- } catch (Exception e)
- {
- e.printStackTrace();
- errors.add(e.getMessage());
- continue;
- }
- lastPdbRequest = pdbRequest;
- if (resultList.getSearchSummary() != null
- && !resultList.getSearchSummary().isEmpty())
- {
- discoveredStructuresSet.addAll(resultList.getSearchSummary());
- }
- }
-
- int noOfStructuresFound = 0;
- String totalTime = (System.currentTimeMillis() - startTime)
- + " milli secs";
- if (discoveredStructuresSet != null
- && !discoveredStructuresSet.isEmpty())
- {
- getResultTable().setModel(
- FTSRestResponse.getTableModel(lastPdbRequest,
- discoveredStructuresSet));
- structuresDiscovered = true;
- noOfStructuresFound = discoveredStructuresSet.size();
- mainFrame.setTitle(MessageManager.formatMessage(
- "label.structure_chooser_no_of_structures",
- noOfStructuresFound, totalTime));
- }
- else
- {
- mainFrame.setTitle(MessageManager
- .getString("label.structure_chooser_manual_association"));
- if (errors.size() > 0)
- {
- StringBuilder errorMsg = new StringBuilder();
- for (String error : errors)
- {
- errorMsg.append(error).append("\n");
- }
- JOptionPane.showMessageDialog(this, errorMsg.toString(),
- MessageManager.getString("label.pdb_web-service_error"),
- JOptionPane.ERROR_MESSAGE);
- }
- }
- }
-
- public void loadLocalCachedPDBEntries()
- {
- ArrayList<CachedPDB> entries = new ArrayList<CachedPDB>();
- for (SequenceI seq : selectedSequences)
- {
- if (seq.getDatasetSequence() != null
- && seq.getDatasetSequence().getAllPDBEntries() != null)
- {
- for (PDBEntry pdbEntry : seq.getDatasetSequence()
- .getAllPDBEntries())
- {
- if (pdbEntry.getFile() != null)
- {
- entries.add(new CachedPDB(seq, pdbEntry));
- }
- }
- }
- }
-
- PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries);
- tbl_local_pdb.setModel(tableModelx);
- }
-
- /**
- * Builds a query string for a given sequences using its DBRef entries
- *
- * @param seq
- * the sequences to build a query for
- * @return the built query string
- */
-
- public static String buildQuery(SequenceI seq)
- {
- boolean isPDBRefsFound = false;
- boolean isUniProtRefsFound = false;
- StringBuilder queryBuilder = new StringBuilder();
- HashSet<String> seqRefs = new LinkedHashSet<String>();
-
- if (seq.getAllPDBEntries() != null)
- {
- for (PDBEntry entry : seq.getAllPDBEntries())
- {
- if (isValidSeqName(entry.getId()))
- {
- queryBuilder.append("pdb_id")
- .append(":")
-.append(entry.getId().toLowerCase())
- .append(" OR ");
- isPDBRefsFound = true;
- // seqRefs.add(entry.getId());
- }
- }
- }
-
- if (seq.getDBRefs() != null && seq.getDBRefs().length != 0)
- {
- for (DBRefEntry dbRef : seq.getDBRefs())
- {
- if (isValidSeqName(getDBRefId(dbRef)))
- {
- if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
- {
- queryBuilder
-.append("uniprot_accession").append(":")
- .append(getDBRefId(dbRef))
- .append(" OR ");
- queryBuilder
-.append("uniprot_id")
- .append(":")
- .append(getDBRefId(dbRef)).append(" OR ");
- isUniProtRefsFound = true;
- }
- else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
- {
-
- queryBuilder.append("pdb_id")
- .append(":").append(getDBRefId(dbRef).toLowerCase())
- .append(" OR ");
- isPDBRefsFound = true;
- }
- else
- {
- seqRefs.add(getDBRefId(dbRef));
- }
- }
- }
- }
-
- if (!isPDBRefsFound && !isUniProtRefsFound)
- {
- String seqName = seq.getName();
- seqName = sanitizeSeqName(seqName);
- String[] names = seqName.toLowerCase().split("\\|");
- for (String name : names)
- {
- // System.out.println("Found name : " + name);
- name.trim();
- if (isValidSeqName(name))
- {
- seqRefs.add(name);
- }
- }
-
- for (String seqRef : seqRefs)
- {
- queryBuilder.append("text:").append(seqRef).append(" OR ");
- }
- }
-
- int endIndex = queryBuilder.lastIndexOf(" OR ");
- if (queryBuilder.toString().length() < 6)
- {
- return null;
- }
- String query = queryBuilder.toString().substring(0, endIndex);
- return query;
- }
-
- /**
- * Remove the following special characters from input string +, -, &, !, (, ),
- * {, }, [, ], ^, ", ~, *, ?, :, \
- *
- * @param seqName
- * @return
- */
- static String sanitizeSeqName(String seqName)
- {
- Objects.requireNonNull(seqName);
- return seqName.replaceAll("\\[\\d*\\]", "")
- .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+");
- }
-
-
- /**
- * Ensures sequence ref names are not less than 3 characters and does not
- * contain a database name
- *
- * @param seqName
- * @return
- */
- public static boolean isValidSeqName(String seqName)
- {
- // System.out.println("seqName : " + seqName);
- String ignoreList = "pdb,uniprot,swiss-prot";
- if (seqName.length() < 3)
- {
- return false;
- }
- if (seqName.contains(":"))
- {
- return false;
- }
- seqName = seqName.toLowerCase();
- for (String ignoredEntry : ignoreList.split(","))
- {
- if (seqName.contains(ignoredEntry))
- {
- return false;
- }
- }
- return true;
- }
-
- public static String getDBRefId(DBRefEntry dbRef)
- {
- String ref = dbRef.getAccessionId().replaceAll("GO:", "");
- return ref;
- }
-
- /**
- * Filters a given list of discovered structures based on supplied argument
- *
- * @param fieldToFilterBy
- * the field to filter by
- */
- public void filterResultSet(final String fieldToFilterBy)
- {
- Thread filterThread = new Thread(new Runnable()
- {
- @Override
- public void run()
- {
- long startTime = System.currentTimeMillis();
- pdbRestCleint = PDBFTSRestClient.getInstance();
- lbl_loading.setVisible(true);
- Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
- .getStructureSummaryFields();
- Collection<FTSData> filteredResponse = new HashSet<FTSData>();
- HashSet<String> errors = new HashSet<String>();
-
- for (SequenceI seq : selectedSequences)
- {
- FTSRestRequest pdbRequest = new FTSRestRequest();
- if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage"))
- {
- pdbRequest.setAllowEmptySeq(false);
- pdbRequest.setResponseSize(1);
- pdbRequest.setFieldToSearchBy("(");
- pdbRequest.setSearchTerm(buildQuery(seq) + ")");
- pdbRequest.setWantedFields(wantedFields);
- pdbRequest.setAssociatedSequence(seq);
- pdbRequest.setFacet(true);
- pdbRequest.setFacetPivot(fieldToFilterBy + ",entry_entity");
- pdbRequest.setFacetPivotMinCount(1);
- }
- else
- {
- pdbRequest.setAllowEmptySeq(false);
- pdbRequest.setResponseSize(1);
- pdbRequest.setFieldToSearchBy("(");
- pdbRequest.setFieldToSortBy(fieldToFilterBy,
- !chk_invertFilter.isSelected());
- pdbRequest.setSearchTerm(buildQuery(seq) + ")");
- pdbRequest.setWantedFields(wantedFields);
- pdbRequest.setAssociatedSequence(seq);
- }
- FTSRestResponse resultList;
- try
- {
- resultList = pdbRestCleint.executeRequest(pdbRequest);
- } catch (Exception e)
- {
- e.printStackTrace();
- errors.add(e.getMessage());
- continue;
- }
- lastPdbRequest = pdbRequest;
- if (resultList.getSearchSummary() != null
- && !resultList.getSearchSummary().isEmpty())
- {
- filteredResponse.addAll(resultList.getSearchSummary());
- }
- }
-
- String totalTime = (System.currentTimeMillis() - startTime)
- + " milli secs";
- if (!filteredResponse.isEmpty())
- {
- final int filterResponseCount = filteredResponse.size();
- Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<FTSData>();
- reorderedStructuresSet.addAll(filteredResponse);
- reorderedStructuresSet.addAll(discoveredStructuresSet);
- getResultTable().setModel(
- FTSRestResponse.getTableModel(
- lastPdbRequest, reorderedStructuresSet));
-
- FTSRestResponse.configureTableColumn(getResultTable(),
- wantedFields);
- getResultTable().getColumn("Ref Sequence").setPreferredWidth(120);
- getResultTable().getColumn("Ref Sequence").setMinWidth(100);
- getResultTable().getColumn("Ref Sequence").setMaxWidth(200);
- // Update table selection model here
- getResultTable().addRowSelectionInterval(0,
- filterResponseCount - 1);
- mainFrame.setTitle(MessageManager.formatMessage(
- "label.structure_chooser_filter_time", totalTime));
- }
- else
- {
- mainFrame.setTitle(MessageManager.formatMessage(
- "label.structure_chooser_filter_time", totalTime));
- if (errors.size() > 0)
- {
- StringBuilder errorMsg = new StringBuilder();
- for (String error : errors)
- {
- errorMsg.append(error).append("\n");
- }
- JOptionPane.showMessageDialog(
- null,
- errorMsg.toString(),
- MessageManager.getString("label.pdb_web-service_error"),
- JOptionPane.ERROR_MESSAGE);
- }
- }
-
- lbl_loading.setVisible(false);
-
- validateSelections();
- }
- });
- filterThread.start();
- }
-
- /**
- * Handles action event for btn_pdbFromFile
- */
- @Override
- public void pdbFromFile_actionPerformed()
- {
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
- chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle(MessageManager.formatMessage(
- "label.select_pdb_file_for",
- selectedSequence.getDisplayId(false)));
- chooser.setToolTipText(MessageManager.formatMessage(
- "label.load_pdb_file_associate_with_sequence",
- selectedSequence.getDisplayId(false)));
-
- int value = chooser.showOpenDialog(null);
- if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
- {
- selectedPdbFileName = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
- validateSelections();
- }
- }
-
- /**
- * Populates the filter combo-box options dynamically depending on discovered
- * structures
- */
- @Override
- protected void populateFilterComboBox()
- {
- if (isStructuresDiscovered())
- {
- cmb_filterOption.addItem(new FilterOption("Best Quality",
- "overall_quality", VIEWS_FILTER));
- cmb_filterOption.addItem(new FilterOption("Best Resolution",
- "resolution", VIEWS_FILTER));
- cmb_filterOption.addItem(new FilterOption("Most Protein Chain",
- "number_of_protein_chains", VIEWS_FILTER));
- cmb_filterOption.addItem(new FilterOption("Most Bound Molecules",
- "number_of_bound_molecules", VIEWS_FILTER));
- cmb_filterOption.addItem(new FilterOption("Most Polymer Residues",
- "number_of_polymer_residues", VIEWS_FILTER));
- }
- cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-",
- VIEWS_ENTER_ID));
- cmb_filterOption.addItem(new FilterOption("From File", "-",
- VIEWS_FROM_FILE));
- cmb_filterOption.addItem(new FilterOption("Cached PDB Entries", "-",
- VIEWS_LOCAL_PDB));
- }
-
- /**
- * Updates the displayed view based on the selected filter option
- */
- @Override
- protected void updateCurrentView()
- {
- FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
- .getSelectedItem());
- layout_switchableViews.show(pnl_switchableViews,
- selectedFilterOpt.getView());
- String filterTitle = mainFrame.getTitle();
- mainFrame.setTitle(frameTitle);
- chk_invertFilter.setVisible(false);
- if (selectedFilterOpt.getView() == VIEWS_FILTER)
- {
- mainFrame.setTitle(filterTitle);
- chk_invertFilter.setVisible(true);
- filterResultSet(selectedFilterOpt.getValue());
- }
- else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
- || selectedFilterOpt.getView() == VIEWS_FROM_FILE)
- {
- mainFrame.setTitle(MessageManager
- .getString("label.structure_chooser_manual_association"));
- idInputAssSeqPanel.loadCmbAssSeq();
- fileChooserAssSeqPanel.loadCmbAssSeq();
- }
- validateSelections();
- }
-
- /**
- * Validates user selection and activates the view button if all parameters
- * are correct
- */
- @Override
- public void validateSelections()
- {
- FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
- .getSelectedItem());
- btn_view.setEnabled(false);
- String currentView = selectedFilterOpt.getView();
- if (currentView == VIEWS_FILTER)
- {
- if (getResultTable().getSelectedRows().length > 0)
- {
- btn_view.setEnabled(true);
- }
- }
- else if (currentView == VIEWS_LOCAL_PDB)
- {
- if (tbl_local_pdb.getSelectedRows().length > 0)
- {
- btn_view.setEnabled(true);
- }
- }
- else if (currentView == VIEWS_ENTER_ID)
- {
- validateAssociationEnterPdb();
- }
- else if (currentView == VIEWS_FROM_FILE)
- {
- validateAssociationFromFile();
- }
- }
-
- /**
- * Validates inputs from the Manual PDB entry panel
- */
- public void validateAssociationEnterPdb()
- {
- AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
- .getCmb_assSeq().getSelectedItem();
- lbl_pdbManualFetchStatus.setIcon(errorImage);
- lbl_pdbManualFetchStatus.setToolTipText("");
- if (txt_search.getText().length() > 0)
- {
- lbl_pdbManualFetchStatus
- .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
- .formatMessage("info.no_pdb_entry_found_for",
- txt_search.getText())));
- }
-
- if (errorWarning.length() > 0)
- {
- lbl_pdbManualFetchStatus.setIcon(warningImage);
- lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(
- true, errorWarning.toString()));
- }
-
- if (selectedSequences.length == 1
- || !assSeqOpt.getName().equalsIgnoreCase(
- "-Select Associated Seq-"))
- {
- txt_search.setEnabled(true);
- if (isValidPBDEntry)
- {
- btn_view.setEnabled(true);
- lbl_pdbManualFetchStatus.setToolTipText("");
- lbl_pdbManualFetchStatus.setIcon(goodImage);
- }
- }
- else
- {
- txt_search.setEnabled(false);
- lbl_pdbManualFetchStatus.setIcon(errorImage);
- }
- }
-
- /**
- * Validates inputs for the manual PDB file selection options
- */
- public void validateAssociationFromFile()
- {
- AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
- .getCmb_assSeq().getSelectedItem();
- lbl_fromFileStatus.setIcon(errorImage);
- if (selectedSequences.length == 1
- || (assSeqOpt != null && !assSeqOpt.getName().equalsIgnoreCase(
- "-Select Associated Seq-")))
- {
- btn_pdbFromFile.setEnabled(true);
- if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
- {
- btn_view.setEnabled(true);
- lbl_fromFileStatus.setIcon(goodImage);
- }
- }
- else
- {
- btn_pdbFromFile.setEnabled(false);
- lbl_fromFileStatus.setIcon(errorImage);
- }
- }
-
- @Override
- public void cmbAssSeqStateChanged()
- {
- validateSelections();
- }
-
- /**
- * Handles the state change event for the 'filter' combo-box and 'invert'
- * check-box
- */
- @Override
- protected void stateChanged(ItemEvent e)
- {
- if (e.getSource() instanceof JCheckBox)
- {
- updateCurrentView();
- }
- else
- {
- if (e.getStateChange() == ItemEvent.SELECTED)
- {
- updateCurrentView();
- }
- }
-
- }
-
- /**
- * Handles action event for btn_ok
- */
- @Override
- public void ok_ActionPerformed()
- {
- final StructureSelectionManager ssm = ap.getStructureSelectionManager();
- new Thread(new Runnable()
- {
- @Override
- public void run()
- {
- FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
- .getSelectedItem());
- String currentView = selectedFilterOpt.getView();
- if (currentView == VIEWS_FILTER)
- {
- int pdbIdColIndex = getResultTable().getColumn("PDB Id")
- .getModelIndex();
- int refSeqColIndex = getResultTable().getColumn("Ref Sequence")
- .getModelIndex();
- int[] selectedRows = getResultTable().getSelectedRows();
- PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
- int count = 0;
- ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
- for (int row : selectedRows)
- {
- String pdbIdStr = getResultTable().getValueAt(row,
- pdbIdColIndex)
- .toString();
- SequenceI selectedSeq = (SequenceI) getResultTable()
- .getValueAt(row,
- refSeqColIndex);
- selectedSeqsToView.add(selectedSeq);
- PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
- if (pdbEntry == null)
- {
- pdbEntry = getFindEntry(pdbIdStr,
- selectedSeq.getAllPDBEntries());
- }
- if (pdbEntry == null)
- {
- pdbEntry = new PDBEntry();
- pdbEntry.setId(pdbIdStr);
- pdbEntry.setType(PDBEntry.Type.PDB);
- selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
- }
- pdbEntriesToView[count++] = pdbEntry;
- }
- SequenceI[] selectedSeqs = selectedSeqsToView
- .toArray(new SequenceI[selectedSeqsToView.size()]);
- launchStructureViewer(ssm, pdbEntriesToView, ap,
- selectedSeqs);
- }
- else if (currentView == VIEWS_LOCAL_PDB)
- {
- int[] selectedRows = tbl_local_pdb.getSelectedRows();
- PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
- int count = 0;
- int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
- .getModelIndex();
- int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
- .getModelIndex();
- ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
- for (int row : selectedRows)
- {
- PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
- pdbIdColIndex);
- pdbEntriesToView[count++] = pdbEntry;
- SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(row,
- refSeqColIndex);
- selectedSeqsToView.add(selectedSeq);
- }
- SequenceI[] selectedSeqs = selectedSeqsToView
- .toArray(new SequenceI[selectedSeqsToView.size()]);
- launchStructureViewer(ssm, pdbEntriesToView, ap,
- selectedSeqs);
- }
- else if (currentView == VIEWS_ENTER_ID)
- {
- SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
- .getCmb_assSeq().getSelectedItem()).getSequence();
- if (userSelectedSeq != null)
- {
- selectedSequence = userSelectedSeq;
- }
-
- String pdbIdStr = txt_search.getText();
- PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
- if (pdbEntry == null)
- {
- pdbEntry = new PDBEntry();
- if (pdbIdStr.split(":").length > 1)
- {
- pdbEntry.setChainCode(pdbIdStr.split(":")[1]);
- }
- pdbEntry.setId(pdbIdStr);
- pdbEntry.setType(PDBEntry.Type.PDB);
- selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
- }
-
- PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
- launchStructureViewer(ssm, pdbEntriesToView, ap,
- new SequenceI[] { selectedSequence });
- }
- else if (currentView == VIEWS_FROM_FILE)
- {
- SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
- .getCmb_assSeq().getSelectedItem()).getSequence();
- if (userSelectedSeq != null)
- {
- selectedSequence = userSelectedSeq;
- }
- PDBEntry fileEntry = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq(selectedPdbFileName,
- jalview.io.AppletFormatAdapter.FILE,
- selectedSequence, true, Desktop.instance);
-
- launchStructureViewer(ssm,
- new PDBEntry[] { fileEntry }, ap,
- new SequenceI[] { selectedSequence });
- }
- mainFrame.dispose();
- }
- }).start();
- }
-
- private PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
- {
- Objects.requireNonNull(id);
- Objects.requireNonNull(pdbEntries);
- PDBEntry foundEntry = null;
- for (PDBEntry entry : pdbEntries)
- {
- if (entry.getId().equalsIgnoreCase(id))
- {
- return entry;
- }
- }
- return foundEntry;
- }
-
- private void launchStructureViewer(StructureSelectionManager ssm,
- final PDBEntry[] pdbEntriesToView,
- final AlignmentPanel alignPanel, SequenceI[] sequences)
- {
- long progressId = sequences.hashCode();
- setProgressBar(MessageManager
- .getString("status.launching_3d_structure_viewer"), progressId);
- final StructureViewer sViewer = new StructureViewer(ssm);
- setProgressBar(null, progressId);
-
- if (SiftsSettings.isMapWithSifts())
- {
- // TODO: prompt user if there are lots of sequences without dbrefs.
- // It can take a long time if we need to fetch all dbrefs for all
- // sequences!
- ArrayList<SequenceI> seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
- for (SequenceI seq : sequences)
- {
- if (seq.getSourceDBRef() == null && seq.getDBRefs() == null)
- {
- seqsWithoutSourceDBRef.add(seq);
- continue;
- }
- }
- if (!seqsWithoutSourceDBRef.isEmpty())
- {
- int y = seqsWithoutSourceDBRef.size();
- setProgressBar(MessageManager.formatMessage(
- "status.fetching_dbrefs_for_sequences_without_valid_refs",
- y,
- progressId);
- SequenceI[] seqWithoutSrcDBRef = new SequenceI[y];
- int x = 0;
- for (SequenceI fSeq : seqsWithoutSourceDBRef)
- {
- seqWithoutSrcDBRef[x++] = fSeq;
- }
- new DBRefFetcher(seqWithoutSrcDBRef).fetchDBRefs(true);
- setProgressBar("Fetch complete.", progressId); // todo i18n
- }
- }
- if (pdbEntriesToView.length > 1)
- {
- ArrayList<SequenceI[]> seqsMap = new ArrayList<SequenceI[]>();
- for (SequenceI seq : sequences)
- {
- seqsMap.add(new SequenceI[] { seq });
- }
- SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
-<<<<<<< Updated upstream
- ssm.setProgressBar(null);
- ssm.setProgressBar(MessageManager
- .getString("status.fetching_3d_structures_for_selected_entries"));
-=======
- setProgressBar("Fetching structure data", progressId);
->>>>>>> Stashed changes
- sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel);
- }
- else
- {
-<<<<<<< Updated upstream
- ssm.setProgressBar(null);
- ssm.setProgressBar(MessageManager.formatMessage(
- "status.fetching_3d_structures_for",
- pdbEntriesToView[0].getId()));
-=======
- setProgressBar(
- "Fetching structure for " + pdbEntriesToView[0].getId(),
- progressId);
->>>>>>> Stashed changes
- sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
- }
- setProgressBar(null, progressId);
- }
-
- /**
- * Populates the combo-box used in associating manually fetched structures to
- * a unique sequence when more than one sequence selection is made.
- */
- @Override
- public void populateCmbAssociateSeqOptions(
- JComboBox<AssociateSeqOptions> cmb_assSeq, JLabel lbl_associateSeq)
- {
- cmb_assSeq.removeAllItems();
- cmb_assSeq.addItem(new AssociateSeqOptions("-Select Associated Seq-",
- null));
- lbl_associateSeq.setVisible(false);
- if (selectedSequences.length > 1)
- {
- for (SequenceI seq : selectedSequences)
- {
- cmb_assSeq.addItem(new AssociateSeqOptions(seq));
- }
- }
- else
- {
- String seqName = selectedSequence.getDisplayId(false);
- seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39);
- lbl_associateSeq.setText(seqName);
- lbl_associateSeq.setVisible(true);
- cmb_assSeq.setVisible(false);
- }
- }
-
- public boolean isStructuresDiscovered()
- {
- return structuresDiscovered;
- }
-
- public void setStructuresDiscovered(boolean structuresDiscovered)
- {
- this.structuresDiscovered = structuresDiscovered;
- }
-
- public Collection<FTSData> getDiscoveredStructuresSet()
- {
- return discoveredStructuresSet;
- }
-
- @Override
- protected void txt_search_ActionPerformed()
- {
- new Thread()
- {
- @Override
- public void run()
- {
- errorWarning.setLength(0);
- isValidPBDEntry = false;
- if (txt_search.getText().length() > 0)
- {
- String searchTerm = txt_search.getText().toLowerCase();
- searchTerm = searchTerm.split(":")[0];
- // System.out.println(">>>>> search term : " + searchTerm);
- List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
- FTSRestRequest pdbRequest = new FTSRestRequest();
- pdbRequest.setAllowEmptySeq(false);
- pdbRequest.setResponseSize(1);
- pdbRequest.setFieldToSearchBy("(pdb_id:");
- pdbRequest.setWantedFields(wantedFields);
- pdbRequest
-.setSearchTerm(searchTerm + ")");
- pdbRequest.setAssociatedSequence(selectedSequence);
- pdbRestCleint = PDBFTSRestClient.getInstance();
- wantedFields.add(pdbRestCleint.getPrimaryKeyColumn());
- FTSRestResponse resultList;
- try
- {
- resultList = pdbRestCleint.executeRequest(pdbRequest);
- } catch (Exception e)
- {
- errorWarning.append(e.getMessage());
- return;
- } finally
- {
- validateSelections();
- }
- if (resultList.getSearchSummary() != null
- && resultList.getSearchSummary().size() > 0)
- {
- isValidPBDEntry = true;
- }
- }
- validateSelections();
- }
- }.start();
- }
-
- @Override
- public void tabRefresh()
- {
- if (selectedSequences != null)
- {
- Thread refreshThread = new Thread(new Runnable()
- {
- @Override
- public void run()
- {
- fetchStructuresMetaData();
- filterResultSet(((FilterOption) cmb_filterOption
- .getSelectedItem()).getValue());
- }
- });
- refreshThread.start();
- }
- }
-
- public class PDBEntryTableModel extends AbstractTableModel
- {
- String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type", "File" };
-
- private List<CachedPDB> pdbEntries;
-
- public PDBEntryTableModel(List<CachedPDB> pdbEntries)
- {
- this.pdbEntries = new ArrayList<CachedPDB>(pdbEntries);
- }
-
- @Override
- public String getColumnName(int columnIndex)
- {
- return columns[columnIndex];
- }
-
- @Override
- public int getRowCount()
- {
- return pdbEntries.size();
- }
-
- @Override
- public int getColumnCount()
- {
- return columns.length;
- }
-
- @Override
- public boolean isCellEditable(int row, int column)
- {
- return false;
- }
-
- @Override
- public Object getValueAt(int rowIndex, int columnIndex)
- {
- Object value = "??";
- CachedPDB entry = pdbEntries.get(rowIndex);
- switch (columnIndex)
- {
- case 0:
- value = entry.getSequence();
- break;
- case 1:
- value = entry.getPdbEntry();
- break;
- case 2:
- value = entry.getPdbEntry().getChainCode() == null ? "_" : entry
- .getPdbEntry().getChainCode();
- break;
- case 3:
- value = entry.getPdbEntry().getType();
- break;
- case 4:
- value = entry.getPdbEntry().getFile();
- break;
- }
- return value;
- }
-
- @Override
- public Class<?> getColumnClass(int columnIndex)
- {
- return columnIndex == 0 ? SequenceI.class : PDBEntry.class;
- }
-
- public CachedPDB getPDBEntryAt(int row)
- {
- return pdbEntries.get(row);
- }
-
- }
-
- private class CachedPDB
- {
- private SequenceI sequence;
-
- private PDBEntry pdbEntry;
-
- public CachedPDB(SequenceI sequence, PDBEntry pdbEntry)
- {
- this.sequence = sequence;
- this.pdbEntry = pdbEntry;
- }
-
- public SequenceI getSequence()
- {
- return sequence;
- }
-
- public PDBEntry getPdbEntry()
- {
- return pdbEntry;
- }
-
- }
-
- private IProgressIndicator progressBar;
-
- @Override
- public void setProgressBar(String message, long id)
- {
- progressBar.setProgressBar(message, id);
- }
-
- @Override
- public void registerHandler(long id, IProgressIndicatorHandler handler)
- {
- progressBar.registerHandler(id, handler);
- }
-
- @Override
- public boolean operationInProgress()
- {
- return progressBar.operationInProgress();
- }
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.gui;
-
-import jalview.analysis.Conservation;
-import jalview.analysis.NJTree;
-import jalview.api.AlignViewportI;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.datamodel.SequenceNode;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.ResidueProperties;
-import jalview.schemes.UserColourScheme;
-import jalview.structure.SelectionSource;
-import jalview.util.Format;
-import jalview.util.MappingUtils;
-import jalview.util.MessageManager;
-
-import java.awt.Color;
-import java.awt.Dimension;
-import java.awt.Font;
-import java.awt.FontMetrics;
-import java.awt.Graphics;
-import java.awt.Graphics2D;
-import java.awt.Point;
-import java.awt.Rectangle;
-import java.awt.RenderingHints;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.awt.event.MouseMotionListener;
-import java.awt.print.PageFormat;
-import java.awt.print.Printable;
-import java.awt.print.PrinterException;
-import java.awt.print.PrinterJob;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.Vector;
-
-import javax.swing.JColorChooser;
-import javax.swing.JPanel;
-import javax.swing.JScrollPane;
-import javax.swing.SwingUtilities;
-import javax.swing.ToolTipManager;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class TreeCanvas extends JPanel implements MouseListener, Runnable,
- Printable, MouseMotionListener, SelectionSource
-{
- /** DOCUMENT ME!! */
- public static final String PLACEHOLDER = " * ";
-
- NJTree tree;
-
- JScrollPane scrollPane;
-
- TreePanel tp;
-
- AlignViewport av;
-
- AlignmentPanel ap;
-
- Font font;
-
- FontMetrics fm;
-
- boolean fitToWindow = true;
-
- boolean showDistances = false;
-
- boolean showBootstrap = false;
-
- boolean markPlaceholders = false;
-
- int offx = 20;
-
- int offy;
-
- float threshold;
-
- String longestName;
-
- int labelLength = -1;
-
- Hashtable nameHash = new Hashtable();
-
- Hashtable nodeHash = new Hashtable();
-
- SequenceNode highlightNode;
-
- boolean applyToAllViews = false;
-
- /**
- * Creates a new TreeCanvas object.
- *
- * @param av
- * DOCUMENT ME!
- * @param tree
- * DOCUMENT ME!
- * @param scroller
- * DOCUMENT ME!
- * @param label
- * DOCUMENT ME!
- */
- public TreeCanvas(TreePanel tp, AlignmentPanel ap, JScrollPane scroller)
- {
- this.tp = tp;
- this.av = ap.av;
- this.ap = ap;
- font = av.getFont();
- scrollPane = scroller;
- addMouseListener(this);
- addMouseMotionListener(this);
- ToolTipManager.sharedInstance().registerComponent(this);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param sequence
- * DOCUMENT ME!
- */
- public void treeSelectionChanged(SequenceI sequence)
- {
- AlignmentPanel[] aps = getAssociatedPanels();
-
- for (int a = 0; a < aps.length; a++)
- {
- SequenceGroup selected = aps[a].av.getSelectionGroup();
-
- if (selected == null)
- {
- selected = new SequenceGroup();
- aps[a].av.setSelectionGroup(selected);
- }
-
- selected.setEndRes(aps[a].av.getAlignment().getWidth() - 1);
- selected.addOrRemove(sequence, true);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param tree
- * DOCUMENT ME!
- */
- public void setTree(NJTree tree)
- {
- this.tree = tree;
- tree.findHeight(tree.getTopNode());
-
- // Now have to calculate longest name based on the leaves
- Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
- boolean has_placeholders = false;
- longestName = "";
-
- for (int i = 0; i < leaves.size(); i++)
- {
- SequenceNode lf = (SequenceNode) leaves.elementAt(i);
-
- if (lf.isPlaceholder())
- {
- has_placeholders = true;
- }
-
- if (longestName.length() < ((Sequence) lf.element()).getName()
- .length())
- {
- longestName = TreeCanvas.PLACEHOLDER
- + ((Sequence) lf.element()).getName();
- }
- }
-
- setMarkPlaceholders(has_placeholders);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param g
- * DOCUMENT ME!
- * @param node
- * DOCUMENT ME!
- * @param chunk
- * DOCUMENT ME!
- * @param scale
- * DOCUMENT ME!
- * @param width
- * DOCUMENT ME!
- * @param offx
- * DOCUMENT ME!
- * @param offy
- * DOCUMENT ME!
- */
- public void drawNode(Graphics g, SequenceNode node, float chunk,
- float scale, int width, int offx, int offy)
- {
- if (node == null)
- {
- return;
- }
-
- if ((node.left() == null) && (node.right() == null))
- {
- // Drawing leaf node
- float height = node.height;
- float dist = node.dist;
-
- int xstart = (int) ((height - dist) * scale) + offx;
- int xend = (int) (height * scale) + offx;
-
- int ypos = (int) (node.ycount * chunk) + offy;
-
- if (node.element() instanceof SequenceI)
- {
- SequenceI seq = (SequenceI) node.element();
-
- if (av.getSequenceColour(seq) == Color.white)
- {
- g.setColor(Color.black);
- }
- else
- {
- g.setColor(av.getSequenceColour(seq).darker());
- }
- }
- else
- {
- g.setColor(Color.black);
- }
-
- // Draw horizontal line
- g.drawLine(xstart, ypos, xend, ypos);
-
- String nodeLabel = "";
-
- if (showDistances && (node.dist > 0))
- {
- nodeLabel = new Format("%-.2f").form(node.dist);
- }
-
- if (showBootstrap && node.bootstrap > -1)
- {
- if (showDistances)
- {
- nodeLabel = nodeLabel + " : ";
- }
-
- nodeLabel = nodeLabel + String.valueOf(node.bootstrap);
- }
-
- if (!nodeLabel.equals(""))
- {
- g.drawString(nodeLabel, xstart + 2, ypos - 2);
- }
-
- String name = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER + node
- .getName()) : node.getName();
-
- int charWidth = fm.stringWidth(name) + 3;
- int charHeight = font.getSize();
-
- Rectangle rect = new Rectangle(xend + 10, ypos - charHeight / 2,
- charWidth, charHeight);
-
- nameHash.put(node.element(), rect);
-
- // Colour selected leaves differently
- SequenceGroup selected = av.getSelectionGroup();
-
- if ((selected != null)
- && selected.getSequences(null).contains(node.element()))
- {
- g.setColor(Color.gray);
-
- g.fillRect(xend + 10, ypos - charHeight / 2, charWidth, charHeight);
- g.setColor(Color.white);
- }
-
- g.drawString(name, xend + 10, ypos + fm.getDescent());
- g.setColor(Color.black);
- }
- else
- {
- drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx,
- offy);
- drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx,
- offy);
-
- float height = node.height;
- float dist = node.dist;
-
- int xstart = (int) ((height - dist) * scale) + offx;
- int xend = (int) (height * scale) + offx;
- int ypos = (int) (node.ycount * chunk) + offy;
-
- g.setColor(node.color.darker());
-
- // Draw horizontal line
- g.drawLine(xstart, ypos, xend, ypos);
- if (node == highlightNode)
- {
- g.fillRect(xend - 3, ypos - 3, 6, 6);
- }
- else
- {
- g.fillRect(xend - 2, ypos - 2, 4, 4);
- }
-
- int ystart = (int) (((SequenceNode) node.left()).ycount * chunk)
- + offy;
- int yend = (int) (((SequenceNode) node.right()).ycount * chunk)
- + offy;
-
- Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);
- nodeHash.put(node, pos);
-
- g.drawLine((int) (height * scale) + offx, ystart,
- (int) (height * scale) + offx, yend);
-
- String nodeLabel = "";
-
- if (showDistances && (node.dist > 0))
- {
- nodeLabel = new Format("%-.2f").form(node.dist);
- }
-
- if (showBootstrap && node.bootstrap > -1)
- {
- if (showDistances)
- {
- nodeLabel = nodeLabel + " : ";
- }
-
- nodeLabel = nodeLabel + String.valueOf(node.bootstrap);
- }
-
- if (!nodeLabel.equals(""))
- {
- g.drawString(nodeLabel, xstart + 2, ypos - 2);
- }
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param x
- * DOCUMENT ME!
- * @param y
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Object findElement(int x, int y)
- {
- Enumeration keys = nameHash.keys();
-
- while (keys.hasMoreElements())
- {
- Object ob = keys.nextElement();
- Rectangle rect = (Rectangle) nameHash.get(ob);
-
- if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y)
- && (y <= (rect.y + rect.height)))
- {
- return ob;
- }
- }
-
- keys = nodeHash.keys();
-
- while (keys.hasMoreElements())
- {
- Object ob = keys.nextElement();
- Rectangle rect = (Rectangle) nodeHash.get(ob);
-
- if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y)
- && (y <= (rect.y + rect.height)))
- {
- return ob;
- }
- }
-
- return null;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param pickBox
- * DOCUMENT ME!
- */
- public void pickNodes(Rectangle pickBox)
- {
- int width = getWidth();
- int height = getHeight();
-
- SequenceNode top = tree.getTopNode();
-
- float wscale = (float) ((width * .8) - (offx * 2))
- / tree.getMaxHeight();
-
- if (top.count == 0)
- {
- top.count = ((SequenceNode) top.left()).count
- + ((SequenceNode) top.right()).count;
- }
-
- float chunk = (float) (height - (offy)) / top.count;
-
- pickNode(pickBox, top, chunk, wscale, width, offx, offy);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param pickBox
- * DOCUMENT ME!
- * @param node
- * DOCUMENT ME!
- * @param chunk
- * DOCUMENT ME!
- * @param scale
- * DOCUMENT ME!
- * @param width
- * DOCUMENT ME!
- * @param offx
- * DOCUMENT ME!
- * @param offy
- * DOCUMENT ME!
- */
- public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,
- float scale, int width, int offx, int offy)
- {
- if (node == null)
- {
- return;
- }
-
- if ((node.left() == null) && (node.right() == null))
- {
- float height = node.height;
- float dist = node.dist;
-
- int xstart = (int) ((height - dist) * scale) + offx;
- int xend = (int) (height * scale) + offx;
-
- int ypos = (int) (node.ycount * chunk) + offy;
-
- if (pickBox.contains(new Point(xend, ypos)))
- {
- if (node.element() instanceof SequenceI)
- {
- SequenceI seq = (SequenceI) node.element();
- SequenceGroup sg = av.getSelectionGroup();
-
- if (sg != null)
- {
- sg.addOrRemove(seq, true);
- }
- }
- }
- }
- else
- {
- pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width,
- offx, offy);
- pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width,
- offx, offy);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param node
- * DOCUMENT ME!
- * @param c
- * DOCUMENT ME!
- */
- public void setColor(SequenceNode node, Color c)
- {
- if (node == null)
- {
- return;
- }
-
- if ((node.left() == null) && (node.right() == null)) // TODO: internal node
- {
- node.color = c;
-
- if (node.element() instanceof SequenceI)
- {
- AlignmentPanel[] aps = getAssociatedPanels();
- if (aps != null)
- {
- for (int a = 0; a < aps.length; a++)
- {
- final SequenceI seq = (SequenceI) node.element();
- aps[a].av.setSequenceColour(seq, c);
- }
- }
- }
- }
- else
- {
- node.color = c;
- setColor((SequenceNode) node.left(), c);
- setColor((SequenceNode) node.right(), c);
- }
- }
-
- /**
- * DOCUMENT ME!
- */
- void startPrinting()
- {
- Thread thread = new Thread(this);
- thread.start();
- }
-
- // put printing in a thread to avoid painting problems
- @Override
- public void run()
- {
- PrinterJob printJob = PrinterJob.getPrinterJob();
- PageFormat pf = printJob.pageDialog(printJob.defaultPage());
-
- printJob.setPrintable(this, pf);
-
- if (printJob.printDialog())
- {
- try
- {
- printJob.print();
- } catch (Exception PrintException)
- {
- PrintException.printStackTrace();
- }
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param pg
- * DOCUMENT ME!
- * @param pf
- * DOCUMENT ME!
- * @param pi
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- *
- * @throws PrinterException
- * DOCUMENT ME!
- */
- @Override
- public int print(Graphics pg, PageFormat pf, int pi)
- throws PrinterException
- {
- pg.setFont(font);
- pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
-
- int pwidth = (int) pf.getImageableWidth();
- int pheight = (int) pf.getImageableHeight();
-
- int noPages = getHeight() / pheight;
-
- if (pi > noPages)
- {
- return Printable.NO_SUCH_PAGE;
- }
-
- if (pwidth > getWidth())
- {
- pwidth = getWidth();
- }
-
- if (fitToWindow)
- {
- if (pheight > getHeight())
- {
- pheight = getHeight();
- }
-
- noPages = 0;
- }
- else
- {
- FontMetrics fm = pg.getFontMetrics(font);
- int height = fm.getHeight() * nameHash.size();
- pg.translate(0, -pi * pheight);
- pg.setClip(0, pi * pheight, pwidth, (pi * pheight) + pheight);
-
- // translate number of pages,
- // height is screen size as this is the
- // non overlapping text size
- pheight = height;
- }
-
- draw(pg, pwidth, pheight);
-
- return Printable.PAGE_EXISTS;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param g
- * DOCUMENT ME!
- */
- @Override
- public void paintComponent(Graphics g)
- {
- super.paintComponent(g);
- g.setFont(font);
-
- if (tree == null)
- {
- g.drawString(MessageManager.getString("label.calculating_tree")
- + "....", 20, getHeight() / 2);
- }
- else
- {
- fm = g.getFontMetrics(font);
-
- if (nameHash.size() == 0)
- {
- repaint();
- }
-
- if (fitToWindow
- || (!fitToWindow && (scrollPane.getHeight() > ((fm
- .getHeight() * nameHash.size()) + offy))))
- {
- draw(g, scrollPane.getWidth(), scrollPane.getHeight());
- setPreferredSize(null);
- }
- else
- {
- setPreferredSize(new Dimension(scrollPane.getWidth(),
- fm.getHeight() * nameHash.size()));
- draw(g, scrollPane.getWidth(), fm.getHeight() * nameHash.size());
- }
-
- scrollPane.revalidate();
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param fontSize
- * DOCUMENT ME!
- */
- @Override
- public void setFont(Font font)
- {
- this.font = font;
- repaint();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param g1
- * DOCUMENT ME!
- * @param width
- * DOCUMENT ME!
- * @param height
- * DOCUMENT ME!
- */
- public void draw(Graphics g1, int width, int height)
- {
- Graphics2D g2 = (Graphics2D) g1;
- g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
- RenderingHints.VALUE_ANTIALIAS_ON);
- g2.setColor(Color.white);
- g2.fillRect(0, 0, width, height);
- g2.setFont(font);
-
- if (longestName == null || tree == null)
- {
- g2.drawString("Calculating tree.", 20, 20);
- }
- offy = font.getSize() + 10;
-
- fm = g2.getFontMetrics(font);
-
- labelLength = fm.stringWidth(longestName) + 20; // 20 allows for scrollbar
-
- float wscale = (width - labelLength - (offx * 2)) / tree.getMaxHeight();
-
- SequenceNode top = tree.getTopNode();
-
- if (top.count == 0)
- {
- top.count = ((SequenceNode) top.left()).count
- + ((SequenceNode) top.right()).count;
- }
-
- float chunk = (float) (height - (offy)) / top.count;
-
- drawNode(g2, tree.getTopNode(), chunk, wscale, width, offx, offy);
-
- if (threshold != 0)
- {
- if (av.getCurrentTree() == tree)
- {
- g2.setColor(Color.red);
- }
- else
- {
- g2.setColor(Color.gray);
- }
-
- int x = (int) ((threshold * (getWidth() - labelLength - (2 * offx))) + offx);
-
- g2.drawLine(x, 0, x, getHeight());
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void mouseReleased(MouseEvent e)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void mouseEntered(MouseEvent e)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void mouseExited(MouseEvent e)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void mouseClicked(MouseEvent evt)
- {
- if (highlightNode != null)
- {
- if (SwingUtilities.isRightMouseButton(evt))
- {
- Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_subtree_colour"),
- highlightNode.color);
- if (col != null)
- {
- setColor(highlightNode, col);
- }
- }
- else if (evt.getClickCount() > 1)
- {
- tree.swapNodes(highlightNode);
- tree.reCount(tree.getTopNode());
- tree.findHeight(tree.getTopNode());
- }
- else
- {
- Vector leaves = new Vector();
- tree.findLeaves(highlightNode, leaves);
-
- for (int i = 0; i < leaves.size(); i++)
- {
- SequenceI seq = (SequenceI) ((SequenceNode) leaves.elementAt(i))
- .element();
- treeSelectionChanged(seq);
- }
- av.sendSelection();
- }
-
- PaintRefresher.Refresh(tp, av.getSequenceSetId());
- repaint();
- }
- }
-
- @Override
- public void mouseMoved(MouseEvent evt)
- {
- av.setCurrentTree(tree);
-
- Object ob = findElement(evt.getX(), evt.getY());
-
- if (ob instanceof SequenceNode)
- {
- highlightNode = (SequenceNode) ob;
- this.setToolTipText("<html>"
- + MessageManager.getString("label.highlightnode"));
- repaint();
-
- }
- else
- {
- if (highlightNode != null)
- {
- highlightNode = null;
- setToolTipText(null);
- repaint();
- }
- }
- }
-
- @Override
- public void mouseDragged(MouseEvent ect)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void mousePressed(MouseEvent e)
- {
- av.setCurrentTree(tree);
-
- int x = e.getX();
- int y = e.getY();
-
- Object ob = findElement(x, y);
-
- if (ob instanceof SequenceI)
- {
- treeSelectionChanged((Sequence) ob);
- PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
- repaint();
- av.sendSelection();
- return;
- }
- else if (!(ob instanceof SequenceNode))
- {
- // Find threshold
- if (tree.getMaxHeight() != 0)
- {
- threshold = (float) (x - offx)
- / (float) (getWidth() - labelLength - (2 * offx));
-
- tree.getGroups().removeAllElements();
- tree.groupNodes(tree.getTopNode(), threshold);
- setColor(tree.getTopNode(), Color.black);
-
- AlignmentPanel[] aps = getAssociatedPanels();
-
- // TODO push calls below into a single AlignViewportI method?
- // see also AlignViewController.deleteGroups
- for (int a = 0; a < aps.length; a++)
- {
- aps[a].av.setSelectionGroup(null);
- aps[a].av.getAlignment().deleteAllGroups();
- aps[a].av.clearSequenceColours();
- if (aps[a].av.getCodingComplement() != null)
- {
- aps[a].av.getCodingComplement().setSelectionGroup(null);
- aps[a].av.getCodingComplement().getAlignment()
- .deleteAllGroups();
- aps[a].av.getCodingComplement().clearSequenceColours();
- }
- }
- colourGroups();
- }
-
- PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
- repaint();
- }
-
- }
-
- void colourGroups()
- {
- AlignmentPanel[] aps = getAssociatedPanels();
- for (int i = 0; i < tree.getGroups().size(); i++)
- {
- Color col = new Color((int) (Math.random() * 255),
- (int) (Math.random() * 255), (int) (Math.random() * 255));
- setColor((SequenceNode) tree.getGroups().elementAt(i), col.brighter());
-
- Vector l = tree.findLeaves(
- (SequenceNode) tree.getGroups().elementAt(i), new Vector());
-
- Vector sequences = new Vector();
-
- for (int j = 0; j < l.size(); j++)
- {
- SequenceI s1 = (SequenceI) ((SequenceNode) l.elementAt(j))
- .element();
-
- if (!sequences.contains(s1))
- {
- sequences.addElement(s1);
- }
- }
-
- ColourSchemeI cs = null;
- SequenceGroup sg = new SequenceGroup(sequences, null, cs, true, true,
- false, 0, av.getAlignment().getWidth() - 1);
-
- if (av.getGlobalColourScheme() != null)
- {
- if (av.getGlobalColourScheme() instanceof UserColourScheme)
- {
- cs = new UserColourScheme(
- ((UserColourScheme) av.getGlobalColourScheme())
- .getColours());
-
- }
- else
- {
- cs = ColourSchemeProperty.getColour(sg, ColourSchemeProperty
- .getColourName(av.getGlobalColourScheme()));
- }
- // cs is null if shading is an annotationColourGradient
- if (cs != null)
- {
- cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
- av.isIgnoreGapsConsensus());
- }
- }
- sg.cs = cs;
- // sg.recalcConservation();
- sg.setName("JTreeGroup:" + sg.hashCode());
- sg.setIdColour(col);
-
- for (int a = 0; a < aps.length; a++)
- {
- if (aps[a].av.getGlobalColourScheme() != null
- && aps[a].av.getGlobalColourScheme().conservationApplied())
- {
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, sg.getSequences(null),
- sg.getStartRes(), sg.getEndRes());
-
- c.calculate();
- c.verdict(false, aps[a].av.getConsPercGaps());
- sg.cs.setConservation(c);
- }
-
- aps[a].av.getAlignment().addGroup(new SequenceGroup(sg));
- // TODO can we push all of the below into AlignViewportI?
- final AlignViewportI codingComplement = aps[a].av
- .getCodingComplement();
- if (codingComplement != null)
- {
- if (codingComplement != null)
- {
- SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg,
- av, codingComplement);
- if (mappedGroup.getSequences().size() > 0)
- {
- codingComplement.getAlignment().addGroup(mappedGroup);
- for (SequenceI seq : mappedGroup.getSequences())
- {
- codingComplement.setSequenceColour(seq, col.brighter());
- }
- }
- }
- }
- }
- }
-
- // notify the panel(s) to redo any group specific stuff.
- for (int a = 0; a < aps.length; a++)
- {
- aps[a].updateAnnotation();
- // TODO: JAL-868 - need to ensure view colour change message is broadcast
- // to any Jmols listening in
- final AlignViewportI codingComplement = aps[a].av
- .getCodingComplement();
- if (codingComplement != null)
- {
- ((AlignViewport) codingComplement).getAlignPanel()
- .updateAnnotation();
-
- }
-
- }
-
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param state
- * DOCUMENT ME!
- */
- public void setShowDistances(boolean state)
- {
- this.showDistances = state;
- repaint();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param state
- * DOCUMENT ME!
- */
- public void setShowBootstrap(boolean state)
- {
- this.showBootstrap = state;
- repaint();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param state
- * DOCUMENT ME!
- */
- public void setMarkPlaceholders(boolean state)
- {
- this.markPlaceholders = state;
- repaint();
- }
-
- AlignmentPanel[] getAssociatedPanels()
- {
- if (applyToAllViews)
- {
- return PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
- }
- else
- {
- return new AlignmentPanel[] { ap };
- }
- }
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.structure;
-
-import jalview.analysis.AlignSeq;
-import jalview.api.StructureSelectionManagerProvider;
-import jalview.commands.CommandI;
-import jalview.commands.EditCommand;
-import jalview.commands.OrderCommand;
-import jalview.datamodel.AlignedCodonFrame;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SearchResults;
-import jalview.datamodel.SequenceI;
-import jalview.gui.IProgressIndicator;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.StructureFile;
-import jalview.util.MappingUtils;
-import jalview.util.MessageManager;
-import jalview.ws.sifts.SiftsClient;
-import jalview.ws.sifts.SiftsException;
-import jalview.ws.sifts.SiftsSettings;
-
-import java.io.PrintStream;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.IdentityHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Vector;
-
-import MCview.Atom;
-import MCview.PDBChain;
-import MCview.PDBfile;
-
-public class StructureSelectionManager
-{
- public final static String NEWLINE = System.lineSeparator();
-
- static IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> instances;
-
- private List<StructureMapping> mappings = new ArrayList<StructureMapping>();
-
- private boolean processSecondaryStructure = false;
-
- private boolean secStructServices = false;
-
- private boolean addTempFacAnnot = false;
-
- private SiftsClient siftsClient = null;
-
- /*
- * Set of any registered mappings between (dataset) sequences.
- */
- private List<AlignedCodonFrame> seqmappings = new ArrayList<AlignedCodonFrame>();
-
- private List<CommandListener> commandListeners = new ArrayList<CommandListener>();
-
- private List<SelectionListener> sel_listeners = new ArrayList<SelectionListener>();
-
- /**
- * @return true if will try to use external services for processing secondary
- * structure
- */
- public boolean isSecStructServices()
- {
- return secStructServices;
- }
-
- /**
- * control use of external services for processing secondary structure
- *
- * @param secStructServices
- */
- public void setSecStructServices(boolean secStructServices)
- {
- this.secStructServices = secStructServices;
- }
-
- /**
- * flag controlling addition of any kind of structural annotation
- *
- * @return true if temperature factor annotation will be added
- */
- public boolean isAddTempFacAnnot()
- {
- return addTempFacAnnot;
- }
-
- /**
- * set flag controlling addition of structural annotation
- *
- * @param addTempFacAnnot
- */
- public void setAddTempFacAnnot(boolean addTempFacAnnot)
- {
- this.addTempFacAnnot = addTempFacAnnot;
- }
-
- /**
- *
- * @return if true, the structure manager will attempt to add secondary
- * structure lines for unannotated sequences
- */
-
- public boolean isProcessSecondaryStructure()
- {
- return processSecondaryStructure;
- }
-
- /**
- * Control whether structure manager will try to annotate mapped sequences
- * with secondary structure from PDB data.
- *
- * @param enable
- */
- public void setProcessSecondaryStructure(boolean enable)
- {
- processSecondaryStructure = enable;
- }
-
- /**
- * debug function - write all mappings to stdout
- */
- public void reportMapping()
- {
- if (mappings.isEmpty())
- {
- System.err.println("reportMapping: No PDB/Sequence mappings.");
- }
- else
- {
- System.err.println("reportMapping: There are " + mappings.size()
- + " mappings.");
- int i = 0;
- for (StructureMapping sm : mappings)
- {
- System.err.println("mapping " + i++ + " : " + sm.pdbfile);
- }
- }
- }
-
- /**
- * map between the PDB IDs (or structure identifiers) used by Jalview and the
- * absolute filenames for PDB data that corresponds to it
- */
- Map<String, String> pdbIdFileName = new HashMap<String, String>();
-
- Map<String, String> pdbFileNameId = new HashMap<String, String>();
-
- public void registerPDBFile(String idForFile, String absoluteFile)
- {
- pdbIdFileName.put(idForFile, absoluteFile);
- pdbFileNameId.put(absoluteFile, idForFile);
- }
-
- public String findIdForPDBFile(String idOrFile)
- {
- String id = pdbFileNameId.get(idOrFile);
- return id;
- }
-
- public String findFileForPDBId(String idOrFile)
- {
- String id = pdbIdFileName.get(idOrFile);
- return id;
- }
-
- public boolean isPDBFileRegistered(String idOrFile)
- {
- return pdbFileNameId.containsKey(idOrFile)
- || pdbIdFileName.containsKey(idOrFile);
- }
-
- private static StructureSelectionManager nullProvider = null;
-
- public static StructureSelectionManager getStructureSelectionManager(
- StructureSelectionManagerProvider context)
- {
- if (context == null)
- {
- if (nullProvider == null)
- {
- if (instances != null)
- {
- throw new Error(
- MessageManager
- .getString("error.implementation_error_structure_selection_manager_null"),
- new NullPointerException(MessageManager
- .getString("exception.ssm_context_is_null")));
- }
- else
- {
- nullProvider = new StructureSelectionManager();
- }
- return nullProvider;
- }
- }
- if (instances == null)
- {
- instances = new java.util.IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager>();
- }
- StructureSelectionManager instance = instances.get(context);
- if (instance == null)
- {
- if (nullProvider != null)
- {
- instance = nullProvider;
- }
- else
- {
- instance = new StructureSelectionManager();
- }
- instances.put(context, instance);
- }
- return instance;
- }
-
- /**
- * flag controlling whether SeqMappings are relayed from received sequence
- * mouse over events to other sequences
- */
- boolean relaySeqMappings = true;
-
- /**
- * Enable or disable relay of seqMapping events to other sequences. You might
- * want to do this if there are many sequence mappings and the host computer
- * is slow
- *
- * @param relay
- */
- public void setRelaySeqMappings(boolean relay)
- {
- relaySeqMappings = relay;
- }
-
- /**
- * get the state of the relay seqMappings flag.
- *
- * @return true if sequence mouse overs are being relayed to other mapped
- * sequences
- */
- public boolean isRelaySeqMappingsEnabled()
- {
- return relaySeqMappings;
- }
-
- Vector listeners = new Vector();
-
- /**
- * register a listener for alignment sequence mouseover events
- *
- * @param svl
- */
- public void addStructureViewerListener(Object svl)
- {
- if (!listeners.contains(svl))
- {
- listeners.addElement(svl);
- }
- }
-
- /**
- * Returns the file name for a mapped PDB id (or null if not mapped).
- *
- * @param pdbid
- * @return
- */
- public String alreadyMappedToFile(String pdbid)
- {
- for (StructureMapping sm : mappings)
- {
- if (sm.getPdbId().equals(pdbid))
- {
- return sm.pdbfile;
- }
- }
- return null;
- }
-
- /**
- * Import structure data and register a structure mapping for broadcasting
- * colouring, mouseovers and selection events (convenience wrapper).
- *
- * @param sequence
- * - one or more sequences to be mapped to pdbFile
- * @param targetChains
- * - optional chain specification for mapping each sequence to pdb
- * (may be nill, individual elements may be nill)
- * @param pdbFile
- * - structure data resource
- * @param protocol
- * - how to resolve data from resource
- * @return null or the structure data parsed as a pdb file
- */
- synchronized public StructureFile setMapping(SequenceI[] sequence,
- String[] targetChains, String pdbFile, String protocol,
- IProgressIndicator progress)
- {
- return computeMapping(true, sequence, targetChains, pdbFile, protocol,
- progress);
- }
-
-
- /**
- * create sequence structure mappings between each sequence and the given
- * pdbFile (retrieved via the given protocol).
- *
- * @param forStructureView
- * when true, record the mapping for use in mouseOvers
- *
- * @param sequenceArray
- * - one or more sequences to be mapped to pdbFile
- * @param targetChainIds
- * - optional chain specification for mapping each sequence to pdb
- * (may be null, individual elements may be null)
- * @param pdbFile
- * - structure data resource
- * @param protocol
- * - how to resolve data from resource
- * @return null or the structure data parsed as a pdb file
- */
- synchronized public StructureFile setMapping(boolean forStructureView,
- SequenceI[] sequenceArray, String[] targetChainIds,
- String pdbFile,
- String protocol)
- {
- return computeMapping(forStructureView, sequenceArray, targetChainIds,
- pdbFile, protocol, null);
- }
-
- synchronized public StructureFile computeMapping(
- boolean forStructureView, SequenceI[] sequenceArray,
- String[] targetChainIds, String pdbFile, String protocol,
- IProgressIndicator progress)
- {
- long progressSessionId = System.currentTimeMillis() * 3;
- /*
- * There will be better ways of doing this in the future, for now we'll use
- * the tried and tested MCview pdb mapping
- */
- boolean parseSecStr = processSecondaryStructure;
- if (isPDBFileRegistered(pdbFile))
- {
- for (SequenceI sq : sequenceArray)
- {
- SequenceI ds = sq;
- while (ds.getDatasetSequence() != null)
- {
- ds = ds.getDatasetSequence();
- }
- ;
- if (ds.getAnnotation() != null)
- {
- for (AlignmentAnnotation ala : ds.getAnnotation())
- {
- // false if any annotation present from this structure
- // JBPNote this fails for jmol/chimera view because the *file* is
- // passed, not the structure data ID -
- if (PDBfile.isCalcIdForFile(ala, findIdForPDBFile(pdbFile)))
- {
- parseSecStr = false;
- }
- }
- }
- }
- }
- StructureFile pdb = null;
- boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
- try
- {
-
- if (pdbFile != null && isCIFFile(pdbFile))
- {
- pdb = new jalview.ext.jmol.JmolParser(addTempFacAnnot, parseSecStr,
- secStructServices, pdbFile, protocol);
- }
- else
- {
- pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
- pdbFile, protocol);
- }
-
- if (pdb.getId() != null && pdb.getId().trim().length() > 0
- && AppletFormatAdapter.FILE.equals(protocol))
- {
- registerPDBFile(pdb.getId().trim(), pdbFile);
- }
- } catch (Exception ex)
- {
- ex.printStackTrace();
- return null;
- }
-
- try
- {
- if (isMapUsingSIFTs)
- {
- siftsClient = new SiftsClient(pdb);
- }
- } catch (SiftsException e)
- {
- isMapUsingSIFTs = false;
- e.printStackTrace();
- }
-
- String targetChainId;
- for (int s = 0; s < sequenceArray.length; s++)
- {
- boolean infChain = true;
- final SequenceI seq = sequenceArray[s];
- if (targetChainIds != null && targetChainIds[s] != null)
- {
- infChain = false;
- targetChainId = targetChainIds[s];
- }
- else if (seq.getName().indexOf("|") > -1)
- {
- targetChainId = seq.getName().substring(
- seq.getName().lastIndexOf("|") + 1);
- if (targetChainId.length() > 1)
- {
- if (targetChainId.trim().length() == 0)
- {
- targetChainId = " ";
- }
- else
- {
- // not a valid chain identifier
- targetChainId = "";
- }
- }
- }
- else
- {
- targetChainId = "";
- }
-
- /*
- * Attempt pairwise alignment of the sequence with each chain in the PDB,
- * and remember the highest scoring chain
- */
- int max = -10;
- AlignSeq maxAlignseq = null;
- String maxChainId = " ";
- PDBChain maxChain = null;
- boolean first = true;
- for (PDBChain chain : pdb.getChains())
- {
- if (targetChainId.length() > 0 && !targetChainId.equals(chain.id)
- && !infChain)
- {
- continue; // don't try to map chains don't match.
- }
- // TODO: correctly determine sequence type for mixed na/peptide
- // structures
- final String type = chain.isNa ? AlignSeq.DNA : AlignSeq.PEP;
- AlignSeq as = AlignSeq.doGlobalNWAlignment(seq, chain.sequence,
- type);
- // equivalent to:
- // AlignSeq as = new AlignSeq(sequence[s], chain.sequence, type);
- // as.calcScoreMatrix();
- // as.traceAlignment();
-
- if (first || as.maxscore > max
- || (as.maxscore == max && chain.id.equals(targetChainId)))
- {
- first = false;
- maxChain = chain;
- max = as.maxscore;
- maxAlignseq = as;
- maxChainId = chain.id;
- }
- }
- if (maxChain == null)
- {
- continue;
- }
-
- if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
- {
- pdbFile = "INLINE" + pdb.getId();
- }
- ArrayList<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
- if (isMapUsingSIFTs)
- {
-<<<<<<< Updated upstream
- setProgressBar(null);
- setProgressBar(MessageManager
- .getString("status.obtaining_mapping_with_sifts"));
-=======
- if (progress!=null) {
- progress.setProgressBar("Obtaining mapping with SIFTS",
- progressSessionId);
- }
->>>>>>> Stashed changes
- jalview.datamodel.Mapping sqmpping = maxAlignseq
- .getMappingFromS1(false);
- if (targetChainId != null && !targetChainId.trim().isEmpty())
- {
- StructureMapping siftsMapping;
- try
- {
- siftsMapping = getStructureMapping(seq, pdbFile, targetChainId,
- pdb, maxChain, sqmpping, maxAlignseq);
- seqToStrucMapping.add(siftsMapping);
- maxChain.makeExactMapping(maxAlignseq, seq);
- maxChain.transferRESNUMFeatures(seq, null);
- maxChain.transferResidueAnnotation(siftsMapping, sqmpping);
- } catch (SiftsException e)
- {
- // fall back to NW alignment
- System.err.println(e.getMessage());
- StructureMapping nwMapping = getNWMappings(seq, pdbFile,
- targetChainId, maxChain, pdb, maxAlignseq);
- seqToStrucMapping.add(nwMapping);
- }
- }
- else
- {
- ArrayList<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
- for (PDBChain chain : pdb.getChains())
- {
- try
- {
- StructureMapping siftsMapping = getStructureMapping(seq,
- pdbFile,
- chain.id, pdb, chain, sqmpping, maxAlignseq);
- foundSiftsMappings.add(siftsMapping);
- } catch (SiftsException e)
- {
- System.err.println(e.getMessage());
- }
- }
- if (!foundSiftsMappings.isEmpty())
- {
- seqToStrucMapping.addAll(foundSiftsMappings);
- maxChain.makeExactMapping(maxAlignseq, seq);
- maxChain.transferRESNUMFeatures(seq, null);
- maxChain.transferResidueAnnotation(foundSiftsMappings.get(0),
- sqmpping);
- }
- else
- {
- StructureMapping nwMapping = getNWMappings(seq, pdbFile,
- maxChainId, maxChain, pdb, maxAlignseq);
- seqToStrucMapping.add(nwMapping);
- }
- }
- }
- else
- {
-<<<<<<< Updated upstream
- setProgressBar(null);
- setProgressBar(MessageManager
- .getString("status.obtaining_mapping_with_nw_alignment"));
-=======
- if (progress != null)
- {
- progress.setProgressBar("Obtaining mapping with NW alignment",
- progressSessionId);
- }
->>>>>>> Stashed changes
- seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId,
- maxChain, pdb, maxAlignseq));
- }
- if (forStructureView)
- {
- mappings.addAll(seqToStrucMapping);
- }
- if (progress != null)
- {
- progress.setProgressBar(null, progressSessionId);
- }
- }
- return pdb;
- }
-
- private boolean isCIFFile(String filename)
- {
- String fileExt = filename.substring(filename.lastIndexOf(".") + 1,
- filename.length());
- return "cif".equalsIgnoreCase(fileExt);
- }
-
- private StructureMapping getStructureMapping(SequenceI seq,
- String pdbFile, String targetChainId, StructureFile pdb,
- PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
- AlignSeq maxAlignseq) throws SiftsException
- {
- StructureMapping curChainMapping = siftsClient
- .getSiftsStructureMapping(seq, pdbFile, targetChainId);
- try
- {
- PDBChain chain = pdb.findChain(targetChainId);
- if (chain != null)
- {
- chain.transferResidueAnnotation(curChainMapping, sqmpping);
- }
- } catch (Exception e)
- {
- e.printStackTrace();
- }
- return curChainMapping;
- }
-
- private StructureMapping getNWMappings(SequenceI seq,
- String pdbFile,
- String maxChainId, PDBChain maxChain, StructureFile pdb,
- AlignSeq maxAlignseq)
- {
- final StringBuilder mappingDetails = new StringBuilder(128);
- mappingDetails.append(NEWLINE).append(
- "Sequence \u27f7 Structure mapping details");
- mappingDetails.append(NEWLINE);
- mappingDetails
- .append("Method: inferred with Needleman & Wunsch alignment");
- mappingDetails.append(NEWLINE).append("PDB Sequence is :")
- .append(NEWLINE).append("Sequence = ")
- .append(maxChain.sequence.getSequenceAsString());
- mappingDetails.append(NEWLINE).append("No of residues = ")
- .append(maxChain.residues.size()).append(NEWLINE)
- .append(NEWLINE);
- PrintStream ps = new PrintStream(System.out)
- {
- @Override
- public void print(String x)
- {
- mappingDetails.append(x);
- }
-
- @Override
- public void println()
- {
- mappingDetails.append(NEWLINE);
- }
- };
-
- maxAlignseq.printAlignment(ps);
-
- mappingDetails.append(NEWLINE).append("PDB start/end ");
- mappingDetails.append(String.valueOf(maxAlignseq.seq2start))
- .append(" ");
- mappingDetails.append(String.valueOf(maxAlignseq.seq2end));
- mappingDetails.append(NEWLINE).append("SEQ start/end ");
- mappingDetails.append(
- String.valueOf(maxAlignseq.seq1start + (seq.getStart() - 1)))
- .append(" ");
- mappingDetails.append(String.valueOf(maxAlignseq.seq1end
- + (seq.getStart() - 1)));
- mappingDetails.append(NEWLINE);
- maxChain.makeExactMapping(maxAlignseq, seq);
- jalview.datamodel.Mapping sqmpping = maxAlignseq
- .getMappingFromS1(false);
- maxChain.transferRESNUMFeatures(seq, null);
-
- HashMap<Integer, int[]> mapping = new HashMap<Integer, int[]>();
- int resNum = -10000;
- int index = 0;
- char insCode = ' ';
-
- do
- {
- Atom tmp = maxChain.atoms.elementAt(index);
- if ((resNum != tmp.resNumber || insCode != tmp.insCode)
- && tmp.alignmentMapping != -1)
- {
- resNum = tmp.resNumber;
- insCode = tmp.insCode;
- if (tmp.alignmentMapping >= -1)
- {
- mapping.put(tmp.alignmentMapping + 1, new int[] { tmp.resNumber,
- tmp.atomIndex });
- }
- }
-
- index++;
- } while (index < maxChain.atoms.size());
-
- StructureMapping nwMapping = new StructureMapping(seq, pdbFile,
- pdb.getId(), maxChainId, mapping, mappingDetails.toString());
- maxChain.transferResidueAnnotation(nwMapping, sqmpping);
- return nwMapping;
- }
-
- public void removeStructureViewerListener(Object svl, String[] pdbfiles)
- {
- listeners.removeElement(svl);
- if (svl instanceof SequenceListener)
- {
- for (int i = 0; i < listeners.size(); i++)
- {
- if (listeners.elementAt(i) instanceof StructureListener)
- {
- ((StructureListener) listeners.elementAt(i))
- .releaseReferences(svl);
- }
- }
- }
-
- if (pdbfiles == null)
- {
- return;
- }
-
- /*
- * Remove mappings to the closed listener's PDB files, but first check if
- * another listener is still interested
- */
- List<String> pdbs = new ArrayList<String>(Arrays.asList(pdbfiles));
-
- StructureListener sl;
- for (int i = 0; i < listeners.size(); i++)
- {
- if (listeners.elementAt(i) instanceof StructureListener)
- {
- sl = (StructureListener) listeners.elementAt(i);
- for (String pdbfile : sl.getPdbFile())
- {
- pdbs.remove(pdbfile);
- }
- }
- }
-
- /*
- * Rebuild the mappings set, retaining only those which are for 'other' PDB
- * files
- */
- if (pdbs.size() > 0)
- {
- List<StructureMapping> tmp = new ArrayList<StructureMapping>();
- for (StructureMapping sm : mappings)
- {
- if (!pdbs.contains(sm.pdbfile))
- {
- tmp.add(sm);
- }
- }
-
- mappings = tmp;
- }
- }
-
- /**
- * Propagate mouseover of a single position in a structure
- *
- * @param pdbResNum
- * @param chain
- * @param pdbfile
- */
- public void mouseOverStructure(int pdbResNum, String chain, String pdbfile)
- {
- AtomSpec atomSpec = new AtomSpec(pdbfile, chain, pdbResNum, 0);
- List<AtomSpec> atoms = Collections.singletonList(atomSpec);
- mouseOverStructure(atoms);
- }
-
- /**
- * Propagate mouseover or selection of multiple positions in a structure
- *
- * @param atoms
- */
- public void mouseOverStructure(List<AtomSpec> atoms)
- {
- if (listeners == null)
- {
- // old or prematurely sent event
- return;
- }
- boolean hasSequenceListener = false;
- for (int i = 0; i < listeners.size(); i++)
- {
- if (listeners.elementAt(i) instanceof SequenceListener)
- {
- hasSequenceListener = true;
- }
- }
- if (!hasSequenceListener)
- {
- return;
- }
-
- SearchResults results = new SearchResults();
- for (AtomSpec atom : atoms)
- {
- SequenceI lastseq = null;
- int lastipos = -1;
- for (StructureMapping sm : mappings)
- {
- if (sm.pdbfile.equals(atom.getPdbFile())
- && sm.pdbchain.equals(atom.getChain()))
- {
- int indexpos = sm.getSeqPos(atom.getPdbResNum());
- if (lastipos != indexpos && lastseq != sm.sequence)
- {
- results.addResult(sm.sequence, indexpos, indexpos);
- lastipos = indexpos;
- lastseq = sm.sequence;
- // construct highlighted sequence list
- for (AlignedCodonFrame acf : seqmappings)
- {
- acf.markMappedRegion(sm.sequence, indexpos, results);
- }
- }
- }
- }
- }
- for (Object li : listeners)
- {
- if (li instanceof SequenceListener)
- {
- ((SequenceListener) li).highlightSequence(results);
- }
- }
- }
-
- /**
- * highlight regions associated with a position (indexpos) in seq
- *
- * @param seq
- * the sequence that the mouse over occurred on
- * @param indexpos
- * the absolute position being mouseovered in seq (0 to seq.length())
- * @param seqPos
- * the sequence position (if -1, seq.findPosition is called to
- * resolve the residue number)
- */
- public void mouseOverSequence(SequenceI seq, int indexpos, int seqPos,
- VamsasSource source)
- {
- boolean hasSequenceListeners = handlingVamsasMo
- || !seqmappings.isEmpty();
- SearchResults results = null;
- if (seqPos == -1)
- {
- seqPos = seq.findPosition(indexpos);
- }
- for (int i = 0; i < listeners.size(); i++)
- {
- Object listener = listeners.elementAt(i);
- if (listener == source)
- {
- // TODO listener (e.g. SeqPanel) is never == source (AlignViewport)
- // Temporary fudge with SequenceListener.getVamsasSource()
- continue;
- }
- if (listener instanceof StructureListener)
- {
- highlightStructure((StructureListener) listener, seq, seqPos);
- }
- else
- {
- if (listener instanceof SequenceListener)
- {
- final SequenceListener seqListener = (SequenceListener) listener;
- if (hasSequenceListeners
- && seqListener.getVamsasSource() != source)
- {
- if (relaySeqMappings)
- {
- if (results == null)
- {
- results = MappingUtils.buildSearchResults(seq, seqPos,
- seqmappings);
- }
- if (handlingVamsasMo)
- {
- results.addResult(seq, seqPos, seqPos);
-
- }
- if (!results.isEmpty())
- {
- seqListener.highlightSequence(results);
- }
- }
- }
- }
- else if (listener instanceof VamsasListener && !handlingVamsasMo)
- {
- ((VamsasListener) listener).mouseOverSequence(seq, indexpos,
- source);
- }
- else if (listener instanceof SecondaryStructureListener)
- {
- ((SecondaryStructureListener) listener).mouseOverSequence(seq,
- indexpos, seqPos);
- }
- }
- }
- }
-
- /**
- * Send suitable messages to a StructureListener to highlight atoms
- * corresponding to the given sequence position(s)
- *
- * @param sl
- * @param seq
- * @param positions
- */
- public void highlightStructure(StructureListener sl, SequenceI seq,
- int... positions)
- {
- if (!sl.isListeningFor(seq))
- {
- return;
- }
- int atomNo;
- List<AtomSpec> atoms = new ArrayList<AtomSpec>();
- for (StructureMapping sm : mappings)
- {
- if (sm.sequence == seq
- || sm.sequence == seq.getDatasetSequence()
- || (sm.sequence.getDatasetSequence() != null && sm.sequence
- .getDatasetSequence() == seq.getDatasetSequence()))
- {
- for (int index : positions)
- {
- atomNo = sm.getAtomNum(index);
-
- if (atomNo > 0)
- {
- atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain, sm
- .getPDBResNum(index), atomNo));
- }
- }
- }
- }
- sl.highlightAtoms(atoms);
- }
-
- /**
- * true if a mouse over event from an external (ie Vamsas) source is being
- * handled
- */
- boolean handlingVamsasMo = false;
-
- long lastmsg = 0;
-
- /**
- * as mouseOverSequence but only route event to SequenceListeners
- *
- * @param sequenceI
- * @param position
- * in an alignment sequence
- */
- public void mouseOverVamsasSequence(SequenceI sequenceI, int position,
- VamsasSource source)
- {
- handlingVamsasMo = true;
- long msg = sequenceI.hashCode() * (1 + position);
- if (lastmsg != msg)
- {
- lastmsg = msg;
- mouseOverSequence(sequenceI, position, -1, source);
- }
- handlingVamsasMo = false;
- }
-
- public Annotation[] colourSequenceFromStructure(SequenceI seq,
- String pdbid)
- {
- return null;
- // THIS WILL NOT BE AVAILABLE IN JALVIEW 2.3,
- // UNTIL THE COLOUR BY ANNOTATION IS REWORKED
- /*
- * Annotation [] annotations = new Annotation[seq.getLength()];
- *
- * StructureListener sl; int atomNo = 0; for (int i = 0; i <
- * listeners.size(); i++) { if (listeners.elementAt(i) instanceof
- * StructureListener) { sl = (StructureListener) listeners.elementAt(i);
- *
- * for (int j = 0; j < mappings.length; j++) {
- *
- * if (mappings[j].sequence == seq && mappings[j].getPdbId().equals(pdbid)
- * && mappings[j].pdbfile.equals(sl.getPdbFile())) {
- * System.out.println(pdbid+" "+mappings[j].getPdbId() +"
- * "+mappings[j].pdbfile);
- *
- * java.awt.Color col; for(int index=0; index<seq.getLength(); index++) {
- * if(jalview.util.Comparison.isGap(seq.getCharAt(index))) continue;
- *
- * atomNo = mappings[j].getAtomNum(seq.findPosition(index)); col =
- * java.awt.Color.white; if (atomNo > 0) { col = sl.getColour(atomNo,
- * mappings[j].getPDBResNum(index), mappings[j].pdbchain,
- * mappings[j].pdbfile); }
- *
- * annotations[index] = new Annotation("X",null,' ',0,col); } return
- * annotations; } } } }
- *
- * return annotations;
- */
- }
-
- public void structureSelectionChanged()
- {
- }
-
- public void sequenceSelectionChanged()
- {
- }
-
- public void sequenceColoursChanged(Object source)
- {
- StructureListener sl;
- for (int i = 0; i < listeners.size(); i++)
- {
- if (listeners.elementAt(i) instanceof StructureListener)
- {
- sl = (StructureListener) listeners.elementAt(i);
- sl.updateColours(source);
- }
- }
- }
-
- public StructureMapping[] getMapping(String pdbfile)
- {
- List<StructureMapping> tmp = new ArrayList<StructureMapping>();
- for (StructureMapping sm : mappings)
- {
- if (sm.pdbfile.equals(pdbfile))
- {
- tmp.add(sm);
- }
- }
- return tmp.toArray(new StructureMapping[tmp.size()]);
- }
-
- /**
- * Returns a readable description of all mappings for the given pdbfile to any
- * of the given sequences
- *
- * @param pdbfile
- * @param seqs
- * @return
- */
- public String printMappings(String pdbfile, List<SequenceI> seqs)
- {
- if (pdbfile == null || seqs == null || seqs.isEmpty())
- {
- return "";
- }
-
- StringBuilder sb = new StringBuilder(64);
- for (StructureMapping sm : mappings)
- {
- if (sm.pdbfile.equals(pdbfile) && seqs.contains(sm.sequence))
- {
- sb.append(sm.mappingDetails);
- sb.append(NEWLINE);
- // separator makes it easier to read multiple mappings
- sb.append("=====================");
- sb.append(NEWLINE);
- }
- }
- sb.append(NEWLINE);
-
- return sb.toString();
- }
-
- /**
- * Remove the given mapping
- *
- * @param acf
- */
- public void deregisterMapping(AlignedCodonFrame acf)
- {
- if (acf != null)
- {
- boolean removed = seqmappings.remove(acf);
- if (removed && seqmappings.isEmpty())
- { // debug
- System.out.println("All mappings removed");
- }
- }
- }
-
- /**
- * Add each of the given codonFrames to the stored set, if not aready present.
- *
- * @param mappings
- */
- public void registerMappings(List<AlignedCodonFrame> mappings)
- {
- if (mappings != null)
- {
- for (AlignedCodonFrame acf : mappings)
- {
- registerMapping(acf);
- }
- }
- }
-
- /**
- * Add the given mapping to the stored set, unless already stored.
- */
- public void registerMapping(AlignedCodonFrame acf)
- {
- if (acf != null)
- {
- if (!seqmappings.contains(acf))
- {
- seqmappings.add(acf);
- }
- }
- }
-
- /**
- * Resets this object to its initial state by removing all registered
- * listeners, codon mappings, PDB file mappings
- */
- public void resetAll()
- {
- if (mappings != null)
- {
- mappings.clear();
- }
- if (seqmappings != null)
- {
- seqmappings.clear();
- }
- if (sel_listeners != null)
- {
- sel_listeners.clear();
- }
- if (listeners != null)
- {
- listeners.clear();
- }
- if (commandListeners != null)
- {
- commandListeners.clear();
- }
- if (view_listeners != null)
- {
- view_listeners.clear();
- }
- if (pdbFileNameId != null)
- {
- pdbFileNameId.clear();
- }
- if (pdbIdFileName != null)
- {
- pdbIdFileName.clear();
- }
- }
-
- public void addSelectionListener(SelectionListener selecter)
- {
- if (!sel_listeners.contains(selecter))
- {
- sel_listeners.add(selecter);
- }
- }
-
- public void removeSelectionListener(SelectionListener toremove)
- {
- if (sel_listeners.contains(toremove))
- {
- sel_listeners.remove(toremove);
- }
- }
-
- public synchronized void sendSelection(
- jalview.datamodel.SequenceGroup selection,
- jalview.datamodel.ColumnSelection colsel, SelectionSource source)
- {
- for (SelectionListener slis : sel_listeners)
- {
- if (slis != source)
- {
- slis.selection(selection, colsel, source);
- }
- }
- }
-
- Vector<AlignmentViewPanelListener> view_listeners = new Vector<AlignmentViewPanelListener>();
-
- public synchronized void sendViewPosition(
- jalview.api.AlignmentViewPanel source, int startRes, int endRes,
- int startSeq, int endSeq)
- {
-
- if (view_listeners != null && view_listeners.size() > 0)
- {
- Enumeration<AlignmentViewPanelListener> listeners = view_listeners
- .elements();
- while (listeners.hasMoreElements())
- {
- AlignmentViewPanelListener slis = listeners.nextElement();
- if (slis != source)
- {
- slis.viewPosition(startRes, endRes, startSeq, endSeq, source);
- }
- ;
- }
- }
- }
-
- /**
- * release all references associated with this manager provider
- *
- * @param jalviewLite
- */
- public static void release(StructureSelectionManagerProvider jalviewLite)
- {
- // synchronized (instances)
- {
- if (instances == null)
- {
- return;
- }
- StructureSelectionManager mnger = (instances.get(jalviewLite));
- if (mnger != null)
- {
- instances.remove(jalviewLite);
- try
- {
- mnger.finalize();
- } catch (Throwable x)
- {
- }
- }
- }
- }
-
- public void registerPDBEntry(PDBEntry pdbentry)
- {
- if (pdbentry.getFile() != null
- && pdbentry.getFile().trim().length() > 0)
- {
- registerPDBFile(pdbentry.getId(), pdbentry.getFile());
- }
- }
-
- public void addCommandListener(CommandListener cl)
- {
- if (!commandListeners.contains(cl))
- {
- commandListeners.add(cl);
- }
- }
-
- public boolean hasCommandListener(CommandListener cl)
- {
- return this.commandListeners.contains(cl);
- }
-
- public boolean removeCommandListener(CommandListener l)
- {
- return commandListeners.remove(l);
- }
-
- /**
- * Forward a command to any command listeners (except for the command's
- * source).
- *
- * @param command
- * the command to be broadcast (in its form after being performed)
- * @param undo
- * if true, the command was being 'undone'
- * @param source
- */
- public void commandPerformed(CommandI command, boolean undo,
- VamsasSource source)
- {
- for (CommandListener listener : commandListeners)
- {
- listener.mirrorCommand(command, undo, this, source);
- }
- }
-
- /**
- * Returns a new CommandI representing the given command as mapped to the
- * given sequences. If no mapping could be made, or the command is not of a
- * mappable kind, returns null.
- *
- * @param command
- * @param undo
- * @param mapTo
- * @param gapChar
- * @return
- */
- public CommandI mapCommand(CommandI command, boolean undo,
- final AlignmentI mapTo, char gapChar)
- {
- if (command instanceof EditCommand)
- {
- return MappingUtils.mapEditCommand((EditCommand) command, undo,
- mapTo, gapChar, seqmappings);
- }
- else if (command instanceof OrderCommand)
- {
- return MappingUtils.mapOrderCommand((OrderCommand) command, undo,
- mapTo, seqmappings);
- }
- return null;
- }
-
- public List<AlignedCodonFrame> getSequenceMappings()
- {
- return seqmappings;
- }
-
-}
+++ /dev/null
-package jalview.util;
-
-import jalview.ext.android.SparseIntArray;
-import jalview.ext.android.SparseShortArray;
-
-/**
- * A class to count occurrences of characters with minimal memory footprint.
- * Sparse arrays of short values are used to hold the counts, with automatic
- * promotion to arrays of int if any count exceeds the maximum value for a
- * short.
- *
- * @author gmcarstairs
- *
- */
-public class SparseCount
-{
- private static final int DEFAULT_PROFILE_SIZE = 2;
-
- /*
- * array of keys (chars) and values (counts)
- * held either as shorts or (if shorts overflow) as ints
- */
- private SparseShortArray shortProfile;
-
- private SparseIntArray intProfile;
-
- /*
- * flag is set true after short overflow occurs
- */
- private boolean useInts;
-
- /**
- * Constructor which initially creates a new sparse array of short values to
- * hold counts.
- *
- * @param profileSize
- */
- public SparseCount(int profileSize)
- {
- this.shortProfile = new SparseShortArray(profileSize);
- }
-
- /**
- * Constructor which allocates an initial count array for only two distinct
- * values (the array will grow if needed)
- */
- public SparseCount()
- {
- this(DEFAULT_PROFILE_SIZE);
- }
-
- /**
- * Adds the given value for the given key (or sets the initial value), and
- * returns the new value
- *
- * @param key
- * @param value
- */
- public int add(int key, int value)
- {
- int newValue = 0;
- if (useInts)
- {
- newValue = intProfile.add(key, value);
- }
- else
- {
- try {
- newValue = shortProfile.add(key, value);
- } catch (ArithmeticException e) {
- handleOverflow();
- newValue = intProfile.add(key, value);
- }
- }
- return newValue;
- }
-
- /**
- * Switch from counting shorts to counting ints
- */
- synchronized void handleOverflow()
- {
- int size = shortProfile.size();
- intProfile = new SparseIntArray(size);
- for (int i = 0; i < size; i++)
- {
- short key = shortProfile.keyAt(i);
- short value = shortProfile.valueAt(i);
- intProfile.put(key, value);
- }
- shortProfile = null;
- useInts = true;
- }
-
- /**
- * Returns the size of the profile (number of distinct items counted)
- *
- * @return
- */
- public int size()
- {
- return useInts ? intProfile.size() : shortProfile.size();
- }
-
- /**
- * Returns the value for the key (zero if no such key)
- *
- * @param key
- * @return
- */
- public int get(int key)
- {
- return useInts ? intProfile.get(key) : shortProfile.get(key);
- }
-
- /**
- * Sets the value for the given key
- *
- * @param key
- * @param value
- */
- public void put(int key, int value)
- {
- if (useInts)
- {
- intProfile.put(key, value);
- }
- else
- {
- shortProfile.put(key, value);
- }
- }
-
- public int keyAt(int k)
- {
- return useInts ? intProfile.keyAt(k) : shortProfile.keyAt(k);
- }
-
- public int valueAt(int k)
- {
- return useInts ? intProfile.valueAt(k) : shortProfile.valueAt(k);
- }
-
- /**
- * Answers true if this object wraps arrays of int values, false if using
- * short values
- *
- * @return
- */
- boolean isUsingInt()
- {
- return useInts;
- }
-}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.ws.dbsources;
-
-import jalview.api.FeatureSettingsModelI;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.io.FormatAdapter;
-import jalview.io.PDBFeatureSettings;
-import jalview.util.MessageManager;
-import jalview.ws.ebi.EBIFetchClient;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Vector;
-
-import com.stevesoft.pat.Regex;
-
-/**
- * @author JimP
- *
- */
-public class Pdb extends EbiFileRetrievedProxy
-{
- public Pdb()
- {
- super();
- }
-
- public static final String FEATURE_INSERTION = "INSERTION";
-
- public static final String FEATURE_RES_NUM = "RESNUM";
-
- private static String currentDefaultFormat = DBRefSource.PDB;
-
- /*
- * (non-Javadoc)
- *
- * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
- */
- @Override
- public String getAccessionSeparator()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see jalview.ws.DbSourceProxy#getAccessionValidator()
- */
- @Override
- public Regex getAccessionValidator()
- {
- return new Regex("([1-9][0-9A-Za-z]{3}):?([ _A-Za-z0-9]?)");
- }
-
- /*
- * (non-Javadoc)
- *
- * @see jalview.ws.DbSourceProxy#getDbSource()
- */
- @Override
- public String getDbSource()
- {
- return DBRefSource.PDB;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see jalview.ws.DbSourceProxy#getDbVersion()
- */
- @Override
- public String getDbVersion()
- {
- return "0";
- }
-
- /*
- * (non-Javadoc)
- *
- * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
- */
- @Override
- public AlignmentI getSequenceRecords(String queries) throws Exception
- {
- AlignmentI pdbAlignment = null;
- Vector result = new Vector();
- String chain = null;
- String id = null;
- if (queries.indexOf(":") > -1)
- {
- chain = queries.substring(queries.indexOf(":") + 1);
- id = queries.substring(0, queries.indexOf(":"));
- }
- else
- {
- id = queries;
- }
- if (queries.length() > 4 && chain == null)
- {
- chain = queries.substring(4, 5);
- id = queries.substring(0, 4);
- }
- if (!isValidReference(id))
- {
- System.err.println("Ignoring invalid pdb query: '" + id + "'");
- stopQuery();
- return null;
- }
- String ext = getCurrentDefaultFormat().equalsIgnoreCase("mmcif") ? ".cif"
- : ".xml";
- EBIFetchClient ebi = new EBIFetchClient();
- file = ebi.fetchDataAsFile("pdb:" + id,
-<<<<<<< HEAD
- getCurrentDefaultFomart().toLowerCase(), ext)
-=======
- getCurrentDefaultFormat().toLowerCase(), "raw", ext)
->>>>>>> develop
- .getAbsolutePath();
- stopQuery();
- if (file == null)
- {
- return null;
- }
- try
- {
-
- pdbAlignment = new FormatAdapter().readFile(file,
- jalview.io.AppletFormatAdapter.FILE,
- getCurrentDefaultFormat());
- if (pdbAlignment != null)
- {
- List<SequenceI> toremove = new ArrayList<SequenceI>();
- for (SequenceI pdbcs : pdbAlignment.getSequences())
- {
- String chid = null;
- // Mapping map=null;
- for (PDBEntry pid : pdbcs.getAllPDBEntries())
- {
- if (pid.getFile() == file)
- {
- chid = pid.getChainCode();
-
- }
- ;
-
- }
- if (chain == null
- || (chid != null && (chid.equals(chain)
- || chid.trim().equals(chain.trim()) || (chain
- .trim().length() == 0 && chid.equals("_")))))
- {
- pdbcs.setName(jalview.datamodel.DBRefSource.PDB + "|" + id
- + "|" + pdbcs.getName());
- // Might need to add more metadata to the PDBEntry object
- // like below
- /*
- * PDBEntry entry = new PDBEntry(); // Construct the PDBEntry
- * entry.setId(id); if (entry.getProperty() == null)
- * entry.setProperty(new Hashtable());
- * entry.getProperty().put("chains", pdbchain.id + "=" +
- * sq.getStart() + "-" + sq.getEnd());
- * sq.getDatasetSequence().addPDBId(entry);
- */
- // Add PDB DB Refs
- // We make a DBRefEtntry because we have obtained the PDB file from
- // a
- // verifiable source
- // JBPNote - PDB DBRefEntry should also carry the chain and mapping
- // information
- DBRefEntry dbentry = new DBRefEntry(getDbSource(),
- getDbVersion(), (chid == null ? id : id + chid));
- // dbentry.setMap()
- pdbcs.addDBRef(dbentry);
- }
- else
- {
- // mark this sequence to be removed from the alignment
- // - since it's not from the right chain
- toremove.add(pdbcs);
- }
- }
- // now remove marked sequences
- for (SequenceI pdbcs : toremove)
- {
- pdbAlignment.deleteSequence(pdbcs);
- if (pdbcs.getAnnotation() != null)
- {
- for (AlignmentAnnotation aa : pdbcs.getAnnotation())
- {
- pdbAlignment.deleteAnnotation(aa);
- }
- }
- }
- }
-
- if (pdbAlignment == null || pdbAlignment.getHeight() < 1)
- {
- throw new Exception(MessageManager.formatMessage(
- "exception.no_pdb_records_for_chain", new String[] { id,
- ((chain == null) ? "' '" : chain) }));
- }
-
- } catch (Exception ex) // Problem parsing PDB file
- {
- stopQuery();
- throw (ex);
- }
- return pdbAlignment;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
- */
- @Override
- public boolean isValidReference(String accession)
- {
- Regex r = getAccessionValidator();
- return r.search(accession.trim());
- }
-
- /**
- * obtain human glyoxalase chain A sequence
- */
- @Override
- public String getTestQuery()
- {
- return "1QIPA";
- }
-
- @Override
- public String getDbName()
- {
- return "PDB"; // getDbSource();
- }
-
- @Override
- public int getTier()
- {
- return 0;
- }
-
- public static String getCurrentDefaultFormat()
- {
- return currentDefaultFormat;
- }
-
- public static void setCurrentDefaultFormat(String currentDefaultFomart)
- {
- Pdb.currentDefaultFormat = currentDefaultFomart;
- }
-
- /**
- * Returns a descriptor for suitable feature display settings with
- * <ul>
- * <li>ResNums or insertions features visible</li>
- * <li>insertions features coloured red</li>
- * <li>ResNum features coloured by label</li>
- * <li>Insertions displayed above (on top of) ResNums</li>
- * </ul>
- */
- @Override
- public FeatureSettingsModelI getFeatureColourScheme()
- {
- return new PDBFeatureSettings();
- }
-}
git://source.jalview.org / jalview.git / commitdiff