From c777b335d0332979123446f431b7f0c160eb4880 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Thu, 4 Jun 2015 11:07:28 +0100 Subject: [PATCH] JAL-1421 generic collections in MCView package (+unit tests) --- src/MCview/AppletPDBCanvas.java | 105 +++++------ src/MCview/Atom.java | 3 - src/MCview/Bond.java | 22 ++- src/MCview/PDBCanvas.java | 125 +++++-------- src/MCview/PDBChain.java | 218 +++++++++++----------- src/MCview/PDBfile.java | 269 ++++++++++++++++----------- src/MCview/Residue.java | 16 +- src/MCview/Zsort.java | 22 ++- test/MCview/AtomTest.java | 63 +++++++ test/MCview/BondTest.java | 24 +++ test/MCview/PDBChainTest.java | 393 +++++++++++++++++++++++++++++++++++++++ test/MCview/PDBfileTest.java | 272 +++++++++++++++++++++++++++ test/MCview/ResidueTest.java | 36 ++++ 13 files changed, 1184 insertions(+), 384 deletions(-) create mode 100644 test/MCview/AtomTest.java create mode 100644 test/MCview/BondTest.java create mode 100644 test/MCview/PDBChainTest.java create mode 100644 test/MCview/PDBfileTest.java create mode 100644 test/MCview/ResidueTest.java diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java index 211cff0..c1c4b2f 100644 --- a/src/MCview/AppletPDBCanvas.java +++ b/src/MCview/AppletPDBCanvas.java @@ -20,18 +20,6 @@ */ package MCview; -import jalview.analysis.AlignSeq; -import jalview.appletgui.AlignmentPanel; -import jalview.appletgui.FeatureRenderer; -import jalview.appletgui.SequenceRenderer; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.SequenceI; -import jalview.structure.AtomSpec; -import jalview.structure.StructureListener; -import jalview.structure.StructureMapping; -import jalview.structure.StructureSelectionManager; -import jalview.util.MessageManager; - import java.awt.Color; import java.awt.Dimension; import java.awt.Event; @@ -49,6 +37,18 @@ import java.io.PrintStream; import java.util.List; import java.util.Vector; +import jalview.analysis.AlignSeq; +import jalview.appletgui.AlignmentPanel; +import jalview.appletgui.FeatureRenderer; +import jalview.appletgui.SequenceRenderer; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.structure.AtomSpec; +import jalview.structure.StructureListener; +import jalview.structure.StructureMapping; +import jalview.structure.StructureSelectionManager; +import jalview.util.MessageManager; + public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotionListener, StructureListener { @@ -127,7 +127,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, PDBChain mainchain; - Vector highlightRes; + Vector highlightRes; boolean pdbAction = false; @@ -284,19 +284,19 @@ public class AppletPDBCanvas extends Panel implements MouseListener, scale = findScale(); } - Vector visiblebonds; + Vector visiblebonds; void setupBonds() { seqColoursReady = false; // Sort the bonds by z coord - visiblebonds = new Vector(); + visiblebonds = new Vector(); for (int ii = 0; ii < pdb.chains.size(); ii++) { if (pdb.chains.elementAt(ii).isVisible) { - Vector tmp = pdb.chains.elementAt(ii).bonds; + Vector tmp = pdb.chains.elementAt(ii).bonds; for (int i = 0; i < tmp.size(); i++) { @@ -327,12 +327,10 @@ public class AppletPDBCanvas extends Panel implements MouseListener, { if (pdb.chains.elementAt(ii).isVisible) { - Vector bonds = pdb.chains.elementAt(ii).bonds; + Vector bonds = pdb.chains.elementAt(ii).bonds; - for (int i = 0; i < bonds.size(); i++) + for (Bond tmp : bonds) { - Bond tmp = (Bond) bonds.elementAt(i); - if (tmp.start[0] >= max[0]) { max[0] = tmp.start[0]; @@ -457,20 +455,15 @@ public class AppletPDBCanvas extends Panel implements MouseListener, { if (pdb.chains.elementAt(ii).isVisible) { - Vector bonds = pdb.chains.elementAt(ii).bonds; + Vector bonds = pdb.chains.elementAt(ii).bonds; bsize += bonds.size(); - for (int i = 0; i < bonds.size(); i++) + for (Bond b : bonds) { - xtot = xtot + ((Bond) bonds.elementAt(i)).start[0] - + ((Bond) bonds.elementAt(i)).end[0]; - - ytot = ytot + ((Bond) bonds.elementAt(i)).start[1] - + ((Bond) bonds.elementAt(i)).end[1]; - - ztot = ztot + ((Bond) bonds.elementAt(i)).start[2] - + ((Bond) bonds.elementAt(i)).end[2]; + xtot = xtot + b.start[0] + b.end[0]; + ytot = ytot + b.start[1] + b.end[1]; + ztot = ztot + b.start[2] + b.end[2]; } } } @@ -588,7 +581,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, for (int i = 0; i < chain.bonds.size(); i++) { - Bond tmp = (Bond) chain.bonds.elementAt(i); + Bond tmp = chain.bonds.elementAt(i); tmp.startCol = Color.lightGray; tmp.endCol = Color.lightGray; if (chain != mainchain) @@ -644,13 +637,13 @@ public class AppletPDBCanvas extends Panel implements MouseListener, zsort = new Zsort(); } - zsort.Zsort(visiblebonds); + zsort.sort(visiblebonds); } Bond tmpBond = null; for (int i = 0; i < visiblebonds.size(); i++) { - tmpBond = (Bond) visiblebonds.elementAt(i); + tmpBond = visiblebonds.elementAt(i); xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) + (getSize().width / 2)); ystart = (int) (((centre[1] - tmpBond.start[1]) * scale) + (getSize().height / 2)); @@ -803,16 +796,18 @@ public class AppletPDBCanvas extends Panel implements MouseListener, { if (highlightRes == null) { - highlightRes = new Vector(); + highlightRes = new Vector(); } - if (highlightRes.contains(fatom.alignmentMapping + "" + "")) + final String atomString = Integer + .toString(fatom.alignmentMapping); + if (highlightRes.contains(atomString)) { - highlightRes.removeElement(fatom.alignmentMapping + ""); + highlightRes.removeElement(atomString); } else { - highlightRes.addElement(fatom.alignmentMapping + ""); + highlightRes.addElement(atomString); } } } @@ -901,14 +896,10 @@ public class AppletPDBCanvas extends Panel implements MouseListener, } // Alter the bonds - for (int ii = 0; ii < pdb.chains.size(); ii++) + for (PDBChain chain : pdb.chains) { - Vector bonds = pdb.chains.elementAt(ii).bonds; - - for (int i = 0; i < bonds.size(); i++) + for (Bond tmpBond : chain.bonds) { - Bond tmpBond = (Bond) bonds.elementAt(i); - // Translate the bond so the centre is 0,0,0 tmpBond.translate(-centre[0], -centre[1], -centre[2]); @@ -942,18 +933,12 @@ public class AppletPDBCanvas extends Panel implements MouseListener, void drawLabels(Graphics g) { - for (int ii = 0; ii < pdb.chains.size(); ii++) + for (PDBChain chain : pdb.chains) { - PDBChain chain = pdb.chains.elementAt(ii); - if (chain.isVisible) { - Vector bonds = pdb.chains.elementAt(ii).bonds; - - for (int i = 0; i < bonds.size(); i++) + for (Bond tmpBond : chain.bonds) { - Bond tmpBond = (Bond) bonds.elementAt(i); - if (tmpBond.at1.isSelected) { labelAtom(g, tmpBond, 1); @@ -961,7 +946,6 @@ public class AppletPDBCanvas extends Panel implements MouseListener, if (tmpBond.at2.isSelected) { - labelAtom(g, tmpBond, 2); } } @@ -1008,11 +992,11 @@ public class AppletPDBCanvas extends Panel implements MouseListener, if (chain.isVisible) { - Vector bonds = pdb.chains.elementAt(ii).bonds; + Vector bonds = pdb.chains.elementAt(ii).bonds; for (int i = 0; i < bonds.size(); i++) { - tmpBond = (Bond) bonds.elementAt(i); + tmpBond = bonds.elementAt(i); truex = (int) (((tmpBond.start[0] - centre[0]) * scale) + (getSize().width / 2)); @@ -1077,7 +1061,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, Bond tmpBond; for (index = 0; index < mainchain.bonds.size(); index++) { - tmpBond = (Bond) mainchain.bonds.elementAt(index); + tmpBond = mainchain.bonds.elementAt(index); if (tmpBond.at1.alignmentMapping == ii - 1) { if (highlightBond1 != null) @@ -1095,13 +1079,13 @@ public class AppletPDBCanvas extends Panel implements MouseListener, if (index > 0) { - highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1); + highlightBond1 = mainchain.bonds.elementAt(index - 1); highlightBond1.at2.isSelected = true; } if (index != mainchain.bonds.size()) { - highlightBond2 = (Bond) mainchain.bonds.elementAt(index); + highlightBond2 = mainchain.bonds.elementAt(index); highlightBond2.at1.isSelected = true; } @@ -1187,7 +1171,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, Bond tmpBond; for (index = 0; index < mainchain.bonds.size(); index++) { - tmpBond = (Bond) mainchain.bonds.elementAt(index); + tmpBond = mainchain.bonds.elementAt(index); if (tmpBond.at1.atomIndex == atomIndex) { if (highlightBond1 != null) @@ -1205,13 +1189,13 @@ public class AppletPDBCanvas extends Panel implements MouseListener, if (index > 0) { - highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1); + highlightBond1 = mainchain.bonds.elementAt(index - 1); highlightBond1.at2.isSelected = true; } if (index != mainchain.bonds.size()) { - highlightBond2 = (Bond) mainchain.bonds.elementAt(index); + highlightBond2 = mainchain.bonds.elementAt(index); highlightBond2.at1.isSelected = true; } @@ -1243,5 +1227,4 @@ public class AppletPDBCanvas extends Panel implements MouseListener, // TODO Auto-generated method stub } - } diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java index 9cbcebb..4d000af 100755 --- a/src/MCview/Atom.java +++ b/src/MCview/Atom.java @@ -111,7 +111,4 @@ public class Atom this.y = y; this.z = z; } - // public void setColor(Color col) { - // this.color = col; - // } } diff --git a/src/MCview/Bond.java b/src/MCview/Bond.java index 18011fb..1f2edd2 100755 --- a/src/MCview/Bond.java +++ b/src/MCview/Bond.java @@ -20,7 +20,7 @@ */ package MCview; -import java.awt.*; +import java.awt.Color; public class Bond { @@ -36,10 +36,12 @@ public class Bond public Atom at2; - public Bond(float[] start, float[] end, Atom at1, Atom at2) + public Bond(Atom at1, Atom at2) { - this.start = start; - this.end = end; + this.start = new float[] + { at1.x, at1.y, at1.z }; + this.end = new float[] + { at2.x, at2.y, at2.z }; this.startCol = at1.color; this.endCol = at2.color; this.at1 = at1; @@ -70,13 +72,13 @@ public class Bond public void translate(float x, float y, float z) { - start[0] = (start[0] + x); - end[0] = (end[0] + x); + start[0] = start[0] + x; + end[0] = end[0] + x; - start[1] = (start[1] + y); - end[1] = (end[1] + y); + start[1] = start[1] + y; + end[1] = end[1] + y; - start[2] = (start[2] + z); - end[2] = (end[2] + z); + start[2] = start[2] + z; + end[2] = end[2] + z; } } diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java index 6f76a25..76bf59b 100644 --- a/src/MCview/PDBCanvas.java +++ b/src/MCview/PDBCanvas.java @@ -20,17 +20,6 @@ */ package MCview; -import jalview.analysis.AlignSeq; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.SequenceI; -import jalview.gui.AlignmentPanel; -import jalview.gui.FeatureRenderer; -import jalview.gui.SequenceRenderer; -import jalview.structure.AtomSpec; -import jalview.structure.StructureListener; -import jalview.structure.StructureMapping; -import jalview.structure.StructureSelectionManager; - import java.awt.Color; import java.awt.Dimension; import java.awt.Event; @@ -52,6 +41,17 @@ import java.util.Vector; import javax.swing.JPanel; import javax.swing.ToolTipManager; +import jalview.analysis.AlignSeq; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.gui.AlignmentPanel; +import jalview.gui.FeatureRenderer; +import jalview.gui.SequenceRenderer; +import jalview.structure.AtomSpec; +import jalview.structure.StructureListener; +import jalview.structure.StructureMapping; +import jalview.structure.StructureSelectionManager; + public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListener, StructureListener { @@ -123,7 +123,7 @@ public class PDBCanvas extends JPanel implements MouseListener, PDBChain mainchain; - Vector highlightRes; + Vector highlightRes; boolean pdbAction = false; @@ -265,23 +265,21 @@ public class PDBCanvas extends JPanel implements MouseListener, ToolTipManager.sharedInstance().setDismissDelay(10000); } - Vector visiblebonds; + Vector visiblebonds; void setupBonds() { seqColoursReady = false; // Sort the bonds by z coord - visiblebonds = new Vector(); + visiblebonds = new Vector(); - for (int ii = 0; ii < pdb.chains.size(); ii++) + for (PDBChain chain : pdb.chains) { - if (pdb.chains.elementAt(ii).isVisible) + if (chain.isVisible) { - Vector tmp = pdb.chains.elementAt(ii).bonds; - - for (int i = 0; i < tmp.size(); i++) + for (Bond bond : chain.bonds) { - visiblebonds.addElement(tmp.elementAt(i)); + visiblebonds.addElement(bond); } } } @@ -305,16 +303,12 @@ public class PDBCanvas extends JPanel implements MouseListener, min[1] = (float) 1e30; min[2] = (float) 1e30; - for (int ii = 0; ii < pdb.chains.size(); ii++) + for (PDBChain chain : pdb.chains) { - if (pdb.chains.elementAt(ii).isVisible) + if (chain.isVisible) { - Vector bonds = pdb.chains.elementAt(ii).bonds; - - for (int i = 0; i < bonds.size(); i++) + for (Bond tmp : chain.bonds) { - Bond tmp = (Bond) bonds.elementAt(i); - if (tmp.start[0] >= max[0]) { max[0] = tmp.start[0]; @@ -440,24 +434,17 @@ public class PDBCanvas extends JPanel implements MouseListener, int bsize = 0; // Find centre coordinate - for (int ii = 0; ii < pdb.chains.size(); ii++) + for (PDBChain chain : pdb.chains) { - if (pdb.chains.elementAt(ii).isVisible) + if (chain.isVisible) { - Vector bonds = pdb.chains.elementAt(ii).bonds; - - bsize += bonds.size(); + bsize += chain.bonds.size(); - for (int i = 0; i < bonds.size(); i++) + for (Bond bond : chain.bonds) { - xtot = xtot + ((Bond) bonds.elementAt(i)).start[0] - + ((Bond) bonds.elementAt(i)).end[0]; - - ytot = ytot + ((Bond) bonds.elementAt(i)).start[1] - + ((Bond) bonds.elementAt(i)).end[1]; - - ztot = ztot + ((Bond) bonds.elementAt(i)).start[2] - + ((Bond) bonds.elementAt(i)).end[2]; + xtot = xtot + bond.start[0] + bond.end[0]; + ytot = ytot + bond.start[1] + bond.end[1]; + ztot = ztot + bond.start[2] + bond.end[2]; } } } @@ -562,7 +549,7 @@ public class PDBCanvas extends JPanel implements MouseListener, for (int i = 0; i < chain.bonds.size(); i++) { - Bond tmp = (Bond) chain.bonds.elementAt(i); + Bond tmp = chain.bonds.elementAt(i); tmp.startCol = Color.lightGray; tmp.endCol = Color.lightGray; if (chain != mainchain) @@ -618,13 +605,13 @@ public class PDBCanvas extends JPanel implements MouseListener, zsort = new Zsort(); } - zsort.Zsort(visiblebonds); + zsort.sort(visiblebonds); } Bond tmpBond = null; for (int i = 0; i < visiblebonds.size(); i++) { - tmpBond = (Bond) visiblebonds.elementAt(i); + tmpBond = visiblebonds.elementAt(i); xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) + (getWidth() / 2)); ystart = (int) (((centre[1] - tmpBond.start[1]) * scale) + (getHeight() / 2)); @@ -779,16 +766,18 @@ public class PDBCanvas extends JPanel implements MouseListener, { if (highlightRes == null) { - highlightRes = new Vector(); + highlightRes = new Vector(); } - if (highlightRes.contains(fatom.alignmentMapping + "")) + final String atomString = Integer + .toString(fatom.alignmentMapping); + if (highlightRes.contains(atomString)) { - highlightRes.remove(fatom.alignmentMapping + ""); + highlightRes.remove(atomString); } else { - highlightRes.add(fatom.alignmentMapping + ""); + highlightRes.add(atomString); } } } @@ -870,14 +859,10 @@ public class PDBCanvas extends JPanel implements MouseListener, } // Alter the bonds - for (int ii = 0; ii < pdb.chains.size(); ii++) + for (PDBChain chain : pdb.chains) { - Vector bonds = pdb.chains.elementAt(ii).bonds; - - for (int i = 0; i < bonds.size(); i++) + for (Bond tmpBond : chain.bonds) { - Bond tmpBond = (Bond) bonds.elementAt(i); - // Translate the bond so the centre is 0,0,0 tmpBond.translate(-centre[0], -centre[1], -centre[2]); @@ -911,18 +896,12 @@ public class PDBCanvas extends JPanel implements MouseListener, void drawLabels(Graphics g) { - for (int ii = 0; ii < pdb.chains.size(); ii++) + for (PDBChain chain : pdb.chains) { - PDBChain chain = pdb.chains.elementAt(ii); - if (chain.isVisible) { - Vector bonds = pdb.chains.elementAt(ii).bonds; - - for (int i = 0; i < bonds.size(); i++) + for (Bond tmpBond : chain.bonds) { - Bond tmpBond = (Bond) bonds.elementAt(i); - if (tmpBond.at1.isSelected) { labelAtom(g, tmpBond, 1); @@ -930,7 +909,6 @@ public class PDBCanvas extends JPanel implements MouseListener, if (tmpBond.at2.isSelected) { - labelAtom(g, tmpBond, 2); } } @@ -975,11 +953,9 @@ public class PDBCanvas extends JPanel implements MouseListener, if (chain.isVisible) { - Vector bonds = pdb.chains.elementAt(ii).bonds; - - for (int i = 0; i < bonds.size(); i++) + for (Bond bond : chain.bonds) { - tmpBond = (Bond) bonds.elementAt(i); + tmpBond = bond; truex = (int) (((tmpBond.start[0] - centre[0]) * scale) + (getWidth() / 2)); @@ -1015,7 +991,7 @@ public class PDBCanvas extends JPanel implements MouseListener, } if (fatom != null) // )&& chain.ds != null) - { + { // dead code? value of chain is either overwritten or discarded chain = pdb.chains.elementAt(foundchain); } } @@ -1041,7 +1017,7 @@ public class PDBCanvas extends JPanel implements MouseListener, Bond tmpBond; for (index = 0; index < mainchain.bonds.size(); index++) { - tmpBond = (Bond) mainchain.bonds.elementAt(index); + tmpBond = mainchain.bonds.elementAt(index); if (tmpBond.at1.alignmentMapping == ii - 1) { if (highlightBond1 != null) @@ -1059,13 +1035,13 @@ public class PDBCanvas extends JPanel implements MouseListener, if (index > 0) { - highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1); + highlightBond1 = mainchain.bonds.elementAt(index - 1); highlightBond1.at2.isSelected = true; } if (index != mainchain.bonds.size()) { - highlightBond2 = (Bond) mainchain.bonds.elementAt(index); + highlightBond2 = mainchain.bonds.elementAt(index); highlightBond2.at1.isSelected = true; } @@ -1153,7 +1129,7 @@ public class PDBCanvas extends JPanel implements MouseListener, Bond tmpBond; for (index = 0; index < mainchain.bonds.size(); index++) { - tmpBond = (Bond) mainchain.bonds.elementAt(index); + tmpBond = mainchain.bonds.elementAt(index); if (tmpBond.at1.atomIndex == atomIndex) { if (highlightBond1 != null) @@ -1171,13 +1147,13 @@ public class PDBCanvas extends JPanel implements MouseListener, if (index > 0) { - highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1); + highlightBond1 = mainchain.bonds.elementAt(index - 1); highlightBond1.at2.isSelected = true; } if (index != mainchain.bonds.size()) { - highlightBond2 = (Bond) mainchain.bonds.elementAt(index); + highlightBond2 = mainchain.bonds.elementAt(index); highlightBond2.at1.isSelected = true; } @@ -1209,5 +1185,4 @@ public class PDBCanvas extends JPanel implements MouseListener, // TODO Auto-generated method stub } - } diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java index 47ed1ef..0e486ac 100755 --- a/src/MCview/PDBChain.java +++ b/src/MCview/PDBChain.java @@ -20,6 +20,10 @@ */ package MCview; +import java.awt.Color; +import java.util.List; +import java.util.Vector; + import jalview.analysis.AlignSeq; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; @@ -27,14 +31,10 @@ import jalview.datamodel.Mapping; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; +import jalview.schemes.ColourSchemeI; import jalview.schemes.ResidueProperties; import jalview.structure.StructureMapping; -import java.awt.Color; -import java.util.Enumeration; -import java.util.List; -import java.util.Vector; - public class PDBChain { /** @@ -46,11 +46,11 @@ public class PDBChain public String id; - public Vector bonds = new Vector(); + public Vector bonds = new Vector(); - public Vector atoms = new Vector(); + public Vector atoms = new Vector(); - public Vector residues = new Vector(); + public Vector residues = new Vector(); public int offset; @@ -104,16 +104,15 @@ public class PDBChain public String print() { - String tmp = ""; + StringBuilder tmp = new StringBuilder(256); - for (int i = 0; i < bonds.size(); i++) + for (Bond b : bonds) { - tmp = tmp + ((Bond) bonds.elementAt(i)).at1.resName + " " - + ((Bond) bonds.elementAt(i)).at1.resNumber + " " + offset - + newline; + tmp.append(b.at1.resName).append(" ").append(b.at1.resNumber) + .append(" ").append(offset).append(newline); } - return tmp; + return tmp.toString(); } /** @@ -129,7 +128,7 @@ public class PDBChain int pdbpos = as.getSeq2Start() - 2; int alignpos = s1.getStart() + as.getSeq1Start() - 3; // first clear out any old alignmentMapping values: - for (Atom atom : (Vector) atoms) + for (Atom atom : atoms) { atom.alignmentMapping = -1; } @@ -148,11 +147,9 @@ public class PDBChain if (as.astr1.charAt(i) == as.astr2.charAt(i)) { - Residue res = (Residue) residues.elementAt(pdbpos); - Enumeration en = res.atoms.elements(); - while (en.hasMoreElements()) + Residue res = residues.elementAt(pdbpos); + for (Atom atom : res.atoms) { - Atom atom = (Atom) en.nextElement(); atom.alignmentMapping = alignpos; } } @@ -196,10 +193,10 @@ public class PDBChain if (features[i].getFeatureGroup().equals(pdbid)) { SequenceFeature tx = new SequenceFeature(features[i]); - tx.setBegin(1 + ((Atom) ((Residue) residues.elementAt(tx.getBegin() - - offset)).atoms.elementAt(0)).alignmentMapping); - tx.setEnd(1 + ((Atom) ((Residue) residues.elementAt(tx.getEnd() - - offset)).atoms.elementAt(0)).alignmentMapping); + tx.setBegin(1 + residues.elementAt(tx.getBegin() + - offset).atoms.elementAt(0).alignmentMapping); + tx.setEnd(1 + residues.elementAt(tx.getEnd() + - offset).atoms.elementAt(0).alignmentMapping); tx.setStatus(status + ((tx.getStatus() == null || tx.getStatus().length() == 0) ? "" : ":" + tx.getStatus())); @@ -212,14 +209,19 @@ public class PDBChain return features; } + /** + * Traverses the list of residues and constructs bonds where CA-to-CA atoms or + * P-to-P atoms are found. Also sets the 'isNa' flag if more than 99% of + * residues contain a P not a CA. + */ public void makeCaBondList() { boolean na = false; int numNa = 0; for (int i = 0; i < (residues.size() - 1); i++) { - Residue tmpres = (Residue) residues.elementAt(i); - Residue tmpres2 = (Residue) residues.elementAt(i + 1); + Residue tmpres = residues.elementAt(i); + Residue tmpres2 = residues.elementAt(i + 1); Atom at1 = tmpres.findAtom("CA"); Atom at2 = tmpres2.findAtom("CA"); na = false; @@ -245,42 +247,57 @@ public class PDBChain System.out.println("not found " + i); } } - if (numNa > 0 && ((numNa / residues.size()) > 0.99)) + + /* + * If > 99% 'P', flag as nucleotide; note the count doesn't include the last + * residue + */ + if (residues.size() > 0 && (numNa / (residues.size() - 1) > 0.99)) { isNa = true; } } + /** + * Construct a bond from atom1 to atom2 and add it to the list of bonds for + * this chain + * + * @param at1 + * @param at2 + */ public void makeBond(Atom at1, Atom at2) { - float[] start = new float[3]; - float[] end = new float[3]; - - start[0] = at1.x; - start[1] = at1.y; - start[2] = at1.z; - - end[0] = at2.x; - end[1] = at2.y; - end[2] = at2.z; - - bonds.addElement(new Bond(start, end, at1, at2)); + bonds.addElement(new Bond(at1, at2)); } + /** + * Traverses the list of atoms and + *
    + *
  • constructs a list of Residues, each containing all the atoms that share + * the same residue number
    • + *
  • adds a RESNUM sequence feature for each position
    • + *
  • creates the sequence string
    • + *
  • determines if nucleotide
    • + *
  • saves the residue number of the first atom as 'offset'
    • + *
  • adds temp factor annotation if the flag is set to do so
    • + *
+ * + * @param visibleChainAnnotation + */ public void makeResidueList(boolean visibleChainAnnotation) { int count = 0; Object symbol; boolean deoxyn = false; boolean nucleotide = false; - StringBuffer seq = new StringBuffer(); - Vector resFeatures = new Vector(); - Vector resAnnotation = new Vector(); + StringBuilder seq = new StringBuilder(256); + Vector resFeatures = new Vector(); + Vector resAnnotation = new Vector(); int i, iSize = atoms.size() - 1; int resNumber = -1; for (i = 0; i <= iSize; i++) { - Atom tmp = (Atom) atoms.elementAt(i); + Atom tmp = atoms.elementAt(i); resNumber = tmp.resNumber; int res = resNumber; @@ -289,17 +306,17 @@ public class PDBChain offset = resNumber; } - Vector resAtoms = new Vector(); + Vector resAtoms = new Vector(); // Add atoms to a vector while the residue number // remains the same as the first atom's resNumber (res) while ((resNumber == res) && (i < atoms.size())) { - resAtoms.addElement(atoms.elementAt(i)); + resAtoms.add(atoms.elementAt(i)); i++; if (i < atoms.size()) { - resNumber = ((Atom) atoms.elementAt(i)).resNumber; + resNumber = atoms.elementAt(i).resNumber; } else { @@ -313,8 +330,8 @@ public class PDBChain // Make a new Residue object with the new atoms vector residues.addElement(new Residue(resAtoms, resNumber - 1, count)); - Residue tmpres = (Residue) residues.lastElement(); - Atom tmpat = (Atom) tmpres.atoms.elementAt(0); + Residue tmpres = residues.lastElement(); + Atom tmpat = tmpres.atoms.get(0); // Make A new SequenceFeature for the current residue numbering SequenceFeature sf = new SequenceFeature("RESNUM", tmpat.resName + ":" + tmpat.resNumIns + " " + pdbid + id, "", offset @@ -373,8 +390,7 @@ public class PDBChain // System.out.println("No of residues = " + residues.size()); for (i = 0, iSize = resFeatures.size(); i < iSize; i++) { - sequence.addSequenceFeature((SequenceFeature) resFeatures - .elementAt(i)); + sequence.addSequenceFeature(resFeatures.elementAt(i)); resFeatures.setElementAt(null, i); } if (visibleChainAnnotation) @@ -383,7 +399,7 @@ public class PDBChain float max = 0; for (i = 0, iSize = annots.length; i < iSize; i++) { - annots[i] = (Annotation) resAnnotation.elementAt(i); + annots[i] = resAnnotation.elementAt(i); if (annots[i].value > max) { max = annots[i].value; @@ -400,81 +416,74 @@ public class PDBChain } } + /** + * Colour start/end of bonds by charge + *
    + *
  • ASP and GLU red
    • + *
  • LYS and ARG blue
    • + *
  • CYS yellow
    • + *
  • others light gray
    • + *
+ */ public void setChargeColours() { - for (int i = 0; i < bonds.size(); i++) + for (Bond b : bonds) { - try + if (b.at1 != null && b.at2 != null) { - Bond b = (Bond) bonds.elementAt(i); - - if (b.at1.resName.equalsIgnoreCase("ASP") - || b.at1.resName.equalsIgnoreCase("GLU")) - { - b.startCol = Color.red; - } - else if (b.at1.resName.equalsIgnoreCase("LYS") - || b.at1.resName.equalsIgnoreCase("ARG")) - { - b.startCol = Color.blue; - } - else if (b.at1.resName.equalsIgnoreCase("CYS")) - { - b.startCol = Color.yellow; - } - else - { - b.startCol = Color.lightGray; - } - - if (b.at2.resName.equalsIgnoreCase("ASP") - || b.at2.resName.equalsIgnoreCase("GLU")) - { - b.endCol = Color.red; - } - else if (b.at2.resName.equalsIgnoreCase("LYS") - || b.at2.resName.equalsIgnoreCase("ARG")) - { - b.endCol = Color.blue; - } - else if (b.at2.resName.equalsIgnoreCase("CYS")) - { - b.endCol = Color.yellow; - } - else - { - b.endCol = Color.lightGray; - } - } catch (Exception e) + b.startCol = getChargeColour(b.at1.resName); + b.endCol = getChargeColour(b.at2.resName); + } + else { - Bond b = (Bond) bonds.elementAt(i); b.startCol = Color.gray; b.endCol = Color.gray; } } } - public void setChainColours(jalview.schemes.ColourSchemeI cs) + public static Color getChargeColour(String resName) + { + Color result = Color.lightGray; + if ("ASP".equals(resName) || "GLU".equals(resName)) + { + result = Color.red; + } + else if ("LYS".equals(resName) || "ARG".equals(resName)) + { + result = Color.blue; + } + else if ("CYS".equals(resName)) + { + result = Color.yellow; + } + return result; + } + + /** + * Sets the start/end colours of bonds to those of the start/end atoms + * according to the specified colour scheme. Note: currently only works for + * peptide residues. + * + * @param cs + */ + public void setChainColours(ColourSchemeI cs) { - Bond b; int index; - for (int i = 0; i < bonds.size(); i++) + for (Bond b : bonds) { try { - b = (Bond) bonds.elementAt(i); - - index = ((Integer) ResidueProperties.aa3Hash.get(b.at1.resName)) + index = ResidueProperties.aa3Hash.get(b.at1.resName) .intValue(); b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0)); - index = ((Integer) ResidueProperties.aa3Hash.get(b.at2.resName)) + index = ResidueProperties.aa3Hash.get(b.at2.resName) .intValue(); b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0)); } catch (Exception e) { - b = (Bond) bonds.elementAt(i); b.startCol = Color.gray; b.endCol = Color.gray; } @@ -483,11 +492,10 @@ public class PDBChain public void setChainColours(Color col) { - for (int i = 0; i < bonds.size(); i++) + for (Bond b : bonds) { - Bond tmp = (Bond) bonds.elementAt(i); - tmp.startCol = col; - tmp.endCol = col; + b.startCol = col; + b.endCol = col; } } diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java index 6ca8711..28ece4c 100755 --- a/src/MCview/PDBfile.java +++ b/src/MCview/PDBfile.java @@ -20,6 +20,14 @@ */ package MCview; +import java.awt.Color; +import java.io.IOException; +import java.lang.reflect.Constructor; +import java.util.ArrayList; +import java.util.Hashtable; +import java.util.List; +import java.util.Vector; + import jalview.analysis.AlignSeq; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; @@ -29,55 +37,58 @@ import jalview.datamodel.SequenceI; import jalview.io.FileParse; import jalview.util.MessageManager; -import java.awt.Color; -import java.io.IOException; -import java.util.ArrayList; -import java.util.Hashtable; -import java.util.List; -import java.util.Vector; - public class PDBfile extends jalview.io.AlignFile { + private static String CALC_ID_PREFIX = "JalviewPDB"; + public Vector chains; public String id; /** - * set to true to add chain alignment annotation as visible annotation. + * set to true to add derived sequence annotations (temp factor read from + * file, or computed secondary structure) to the alignment */ - boolean VisibleChainAnnotation = false; + private boolean visibleChainAnnotation = false; - boolean processSecondaryStructure = true; + /* + * Set true to predict secondary structure (using JMol for protein, Annotate3D + * for RNA) + */ + private boolean predictSecondaryStructure = true; - boolean externalSecondaryStructure = false; + /* + * Set true (with predictSecondaryStructure=true) to predict secondary + * structure using an external service (currently Annotate3D for RNA only) + */ + private boolean externalSecondaryStructure = false; - public PDBfile(boolean visibleChainAnnotation, - boolean processSecondaryStructure, boolean externalSecStr) + public PDBfile(boolean addAlignmentAnnotations, boolean predictSecondaryStructure, + boolean externalSecStr) { super(); - VisibleChainAnnotation = visibleChainAnnotation; - this.processSecondaryStructure = processSecondaryStructure; + this.visibleChainAnnotation = addAlignmentAnnotations; + this.predictSecondaryStructure = predictSecondaryStructure; this.externalSecondaryStructure = externalSecStr; } - public PDBfile(boolean visibleChainAnnotation, - boolean processSecondaryStructure, boolean externalSecStr, - String file, String protocol) throws IOException + public PDBfile(boolean addAlignmentAnnotations, boolean predictSecondaryStructure, + boolean externalSecStr, String file, String protocol) + throws IOException { super(false, file, protocol); - VisibleChainAnnotation = visibleChainAnnotation; - this.processSecondaryStructure = processSecondaryStructure; + this.visibleChainAnnotation = addAlignmentAnnotations; + this.predictSecondaryStructure = predictSecondaryStructure; this.externalSecondaryStructure = externalSecStr; doParse(); } - public PDBfile(boolean visibleChainAnnotation, - boolean processSecondaryStructure, boolean externalSecStr, - FileParse source) throws IOException + public PDBfile(boolean addAlignmentAnnotations, boolean predictSecondaryStructure, + boolean externalSecStr, FileParse source) throws IOException { super(false, source); - VisibleChainAnnotation = visibleChainAnnotation; - this.processSecondaryStructure = processSecondaryStructure; + this.visibleChainAnnotation = addAlignmentAnnotations; + this.predictSecondaryStructure = predictSecondaryStructure; this.externalSecondaryStructure = externalSecStr; doParse(); } @@ -92,15 +103,16 @@ public class PDBfile extends jalview.io.AlignFile // TODO set the filename sensibly - try using data source name. id = safeName(getDataName()); - chains = new Vector(); - ArrayList rna = new ArrayList(), prot = new ArrayList(); + chains = new Vector(); + List rna = new ArrayList(); + List prot = new ArrayList(); PDBChain tmpchain; String line = null; boolean modelFlag = false; boolean terFlag = false; String lastID = ""; - int index = 0; + int indexx = 0; String atomnam = null; try { @@ -186,34 +198,10 @@ public class PDBfile extends jalview.io.AlignFile { id = inFile.getName(); } - for (int i = 0; i < chains.size(); i++) + for (PDBChain chain : chains) { - SequenceI dataset = chains.elementAt(i).sequence; - dataset.setName(id + "|" + dataset.getName()); - PDBEntry entry = new PDBEntry(); - entry.setId(id); - entry.setType(PDBEntry.Type.PDB); - entry.setProperty(new Hashtable()); - if (chains.elementAt(i).id != null) - { - // entry.getProperty().put("CHAIN", chains.elementAt(i).id); - entry.setChainCode(String.valueOf(chains.elementAt(i).id)); - } - if (inFile != null) - { - entry.setFile(inFile.getAbsolutePath()); - } - else - { - // TODO: decide if we should dump the datasource to disk - entry.setFile(getDataName()); - } - dataset.addPDBId(entry); - SequenceI chainseq = dataset.deriveSequence(); // PDBChain objects - // maintain reference to - // dataset - seqs.addElement(chainseq); - if (isRNA(chainseq) == true) + SequenceI chainseq = postProcessChain(chain); + if (isRNA(chainseq)) { rna.add(chainseq); } @@ -221,47 +209,10 @@ public class PDBfile extends jalview.io.AlignFile { prot.add(chainseq); } - - AlignmentAnnotation[] chainannot = chainseq.getAnnotation(); - - if (chainannot != null && VisibleChainAnnotation) - { - for (int ai = 0; ai < chainannot.length; ai++) - { - chainannot[ai].visible = VisibleChainAnnotation; - annotations.addElement(chainannot[ai]); - } - } } - if (processSecondaryStructure) + if (predictSecondaryStructure) { - if (externalSecondaryStructure && rna.size() > 0) - { - try - { - processPdbFileWithAnnotate3d(rna); - } catch (Exception x) - { - System.err - .println("Exceptions when dealing with RNA in pdb file"); - x.printStackTrace(); - - } - } - ; - if (prot.size() > 0) - { - try - { - processPdbFileWithJmol(prot); - } catch (Exception x) - { - System.err - .println("Exceptions from Jmol when processing data in pdb file"); - x.printStackTrace(); - - } - } + predictSecondaryStructure(rna, prot); } } catch (OutOfMemoryError er) { @@ -280,27 +231,117 @@ public class PDBfile extends jalview.io.AlignFile markCalcIds(); } - private static String calcIdPrefix = "JalviewPDB"; + /** + * Predict secondary structure for RNA and/or protein sequences and add as + * annotations + * + * @param rnaSequences + * @param proteinSequences + */ + protected void predictSecondaryStructure(List rnaSequences, + List proteinSequences) + { + /* + * Currently using Annotate3D for RNA, but only if the 'use external + * prediction' flag is set + */ + if (externalSecondaryStructure && rnaSequences.size() > 0) + { + try + { + processPdbFileWithAnnotate3d(rnaSequences); + } catch (Exception x) + { + System.err + .println("Exceptions when dealing with RNA in pdb file"); + x.printStackTrace(); + + } + } + + /* + * Currently using JMol PDB parser for peptide + */ + if (proteinSequences.size() > 0) + { + try + { + processPdbFileWithJmol(proteinSequences); + } catch (Exception x) + { + System.err + .println("Exceptions from Jmol when processing data in pdb file"); + x.printStackTrace(); + } + } + } + + /** + * Process a parsed chain to construct and return a Sequence, and add it to + * the list of sequences parsed. + * + * @param chain + * @return + */ + protected SequenceI postProcessChain(PDBChain chain) + { + SequenceI dataset = chain.sequence; + dataset.setName(id + "|" + dataset.getName()); + PDBEntry entry = new PDBEntry(); + entry.setId(id); + entry.setType(PDBEntry.Type.PDB); + entry.setProperty(new Hashtable()); + if (chain.id != null) + { + // entry.getProperty().put("CHAIN", chains.elementAt(i).id); + entry.setChainCode(String.valueOf(chain.id)); + } + if (inFile != null) + { + entry.setFile(inFile.getAbsolutePath()); + } + else + { + // TODO: decide if we should dump the datasource to disk + entry.setFile(getDataName()); + } + dataset.addPDBId(entry); + // PDBChain objects maintain reference to dataset + SequenceI chainseq = dataset.deriveSequence(); + seqs.addElement(chainseq); + + AlignmentAnnotation[] chainannot = chainseq.getAnnotation(); + + if (chainannot != null && visibleChainAnnotation) + { + for (int ai = 0; ai < chainannot.length; ai++) + { + chainannot[ai].visible = visibleChainAnnotation; + annotations.addElement(chainannot[ai]); + } + } + return chainseq; + } public static boolean isCalcIdHandled(String calcId) { - return calcId != null && (calcIdPrefix.equals(calcId)); + return calcId != null && (CALC_ID_PREFIX.equals(calcId)); } public static boolean isCalcIdForFile(AlignmentAnnotation alan, String pdbFile) { return alan.getCalcId() != null - && calcIdPrefix.equals(alan.getCalcId()) + && CALC_ID_PREFIX.equals(alan.getCalcId()) && pdbFile.equals(alan.getProperty("PDBID")); } public static String relocateCalcId(String calcId, Hashtable alreadyLoadedPDB) throws Exception { - int s = calcIdPrefix.length(), end = calcId.indexOf(calcIdPrefix, s); + int s = CALC_ID_PREFIX.length(), end = calcId.indexOf(CALC_ID_PREFIX, s); String between = calcId.substring(s, end - 1); - return calcIdPrefix + alreadyLoadedPDB.get(between) + ":" + return CALC_ID_PREFIX + alreadyLoadedPDB.get(between) + ":" + calcId.substring(end); } @@ -317,7 +358,7 @@ public class PDBfile extends jalview.io.AlignFile { oldId = ""; } - aa.setCalcId(calcIdPrefix); + aa.setCalcId(CALC_ID_PREFIX); aa.setProperty("PDBID", id); aa.setProperty("oldCalcId", oldId); } @@ -325,7 +366,7 @@ public class PDBfile extends jalview.io.AlignFile } } - private void processPdbFileWithJmol(ArrayList prot) + private void processPdbFileWithJmol(List prot) throws Exception { try @@ -333,14 +374,16 @@ public class PDBfile extends jalview.io.AlignFile Class cl = Class.forName("jalview.ext.jmol.PDBFileWithJmol"); if (cl != null) { - Object jmf = cl.getConstructor(new Class[] - { FileParse.class }).newInstance(new Object[] - { new FileParse(getDataName(), type) }); - Alignment al = new Alignment((SequenceI[]) cl.getMethod( + final Constructor constructor = cl.getConstructor(new Class[] + { FileParse.class }); + final Object[] args = new Object[] + { new FileParse(getDataName(), type) }; + Object jmf = constructor.newInstance(args); + AlignmentI al = new Alignment((SequenceI[]) cl.getMethod( "getSeqsAsArray", new Class[] {}).invoke(jmf)); cl.getMethod("addAnnotations", new Class[] - { Alignment.class }).invoke(jmf, al); + { AlignmentI.class }).invoke(jmf, al); for (SequenceI sq : al.getSequences()) { if (sq.getDatasetSequence() != null) @@ -359,7 +402,7 @@ public class PDBfile extends jalview.io.AlignFile } } - private void replaceAndUpdateChains(ArrayList prot, + private void replaceAndUpdateChains(List prot, AlignmentI al, String pep, boolean b) { List> replaced = AlignSeq @@ -388,7 +431,7 @@ public class PDBfile extends jalview.io.AlignFile } } - private void processPdbFileWithAnnotate3d(ArrayList rna) + private void processPdbFileWithAnnotate3d(List rna) throws Exception { // System.out.println("this is a PDB format and RNA sequence"); @@ -455,7 +498,7 @@ public class PDBfile extends jalview.io.AlignFile { for (int i = 0; i < chains.size(); i++) { - chains.elementAt(i).makeResidueList(VisibleChainAnnotation); + chains.elementAt(i).makeResidueList(visibleChainAnnotation); } } @@ -500,17 +543,17 @@ public class PDBfile extends jalview.io.AlignFile { for (int i = 0; i < chains.size(); i++) { + // divide by zero --> infinity --> 255 ;-) chains.elementAt(i).setChainColours( Color.getHSBColor(1.0f / i, .4f, 1.0f)); } } - public boolean isRNA(SequenceI seqs) + public static boolean isRNA(SequenceI seq) { - for (int i = 0; i < seqs.getLength(); i++) + for (char c : seq.getSequence()) { - if ((seqs.getCharAt(i) != 'A') && (seqs.getCharAt(i) != 'C') - && (seqs.getCharAt(i) != 'G') && (seqs.getCharAt(i) != 'U')) + if ((c != 'A') && (c != 'C') && (c != 'G') && (c != 'U')) { return false; } diff --git a/src/MCview/Residue.java b/src/MCview/Residue.java index 977323d..abb29a8 100755 --- a/src/MCview/Residue.java +++ b/src/MCview/Residue.java @@ -20,32 +20,30 @@ */ package MCview; -import java.util.*; +import java.util.Vector; public class Residue { - Vector atoms = new Vector(); + Vector atoms; int number; int count; - int seqnumber; - - public Residue(Vector atoms, int number, int count) + public Residue(Vector resAtoms, int number, int count) { - this.atoms = atoms; + this.atoms = resAtoms; this.number = number; this.count = count; } public Atom findAtom(String name) { - for (int i = 0; i < atoms.size(); i++) + for (Atom atom : atoms) { - if (((Atom) atoms.elementAt(i)).name.equals(name)) + if (atom.name.equals(name)) { - return (Atom) atoms.elementAt(i); + return atom; } } diff --git a/src/MCview/Zsort.java b/src/MCview/Zsort.java index 654eb80..20f034c 100755 --- a/src/MCview/Zsort.java +++ b/src/MCview/Zsort.java @@ -20,16 +20,22 @@ */ package MCview; -import java.util.*; +import java.util.Vector; public class Zsort { - public void Zsort(Vector bonds) + /** + * Sorts the Bond list in ascending order of the z-value of the bond start + * atom + * + * @param bonds + */ + public void sort(Vector bonds) { sort(bonds, 0, bonds.size() - 1); } - public void sort(Vector bonds, int p, int r) + public void sort(Vector bonds, int p, int r) { int q; @@ -41,9 +47,9 @@ public class Zsort } } - private int partition(Vector bonds, int p, int r) + private int partition(Vector bonds, int p, int r) { - float x = ((Bond) bonds.elementAt(p)).start[2]; + float x = bonds.elementAt(p).start[2]; int i = p - 1; int j = r + 1; Bond tmp; @@ -52,17 +58,17 @@ public class Zsort do { j--; - } while ((j >= 0) && (((Bond) bonds.elementAt(j)).start[2] > x)); + } while ((j >= 0) && (bonds.elementAt(j).start[2] > x)); do { i++; } while ((i < bonds.size()) - && (((Bond) bonds.elementAt(i)).start[2] < x)); + && (bonds.elementAt(i).start[2] < x)); if (i < j) { - tmp = (Bond) bonds.elementAt(i); + tmp = bonds.elementAt(i); bonds.setElementAt(bonds.elementAt(j), i); bonds.setElementAt(tmp, j); } diff --git a/test/MCview/AtomTest.java b/test/MCview/AtomTest.java new file mode 100644 index 0000000..8c271b3 --- /dev/null +++ b/test/MCview/AtomTest.java @@ -0,0 +1,63 @@ +package MCview; + +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.fail; + +import org.junit.Test; + +public class AtomTest +{ + + /** + * Test the constructor that parses a PDB file format ATOM line. Fields are in + * fixed column positions + */ + @Test + public void testStringConstructor() + { + Atom a = new Atom( + "ATOM 349 NE2 GLN A 48 22.290 8.595 17.680 1.00 14.30 N"); + assertEquals(349, a.atomIndex); + assertEquals("NE", a.name); + assertEquals("GLN", a.resName); + assertEquals("A", a.chain); + assertEquals(48, a.resNumber); + assertEquals("48", a.resNumIns); + assertEquals(' ', a.insCode); + assertEquals(22.290, a.x, 0.00001); + assertEquals(8.595, a.y, 0.00001); + assertEquals(17.680, a.z, 0.00001); + assertEquals(1f, a.occupancy, 0.00001); + assertEquals(14.3, a.tfactor, 0.00001); + } + + /** + * Test the case where occupancy and temp factor are blank - should default to + * 1 + */ + @Test + public void testStringConstructor_blankOccupancyTempFactor() + { + Atom a = new Atom( + "ATOM 349 NE2 GLN A 48 22.290 8.595 17.680 N"); + assertEquals(1f, a.occupancy, 0.00001); + assertEquals(1f, a.tfactor, 0.00001); + } + + /** + * Parsing non-numeric data as Atom throws an exception + */ + @Test + public void testStringConstructor_malformed() + { + try + { + new Atom( + "ATOM 34N NE2 GLN A 48 22.290 8.595 17.680 1.00 14.30 N"); + fail("Expected exception"); + } catch (NumberFormatException e) + { + // expected + } + } +} \ No newline at end of file diff --git a/test/MCview/BondTest.java b/test/MCview/BondTest.java new file mode 100644 index 0000000..333bfce --- /dev/null +++ b/test/MCview/BondTest.java @@ -0,0 +1,24 @@ +package MCview; + +import static org.junit.Assert.assertEquals; + +import org.junit.Test; + +public class BondTest +{ + + @Test + public void testTranslate() + { + Atom a1 = new Atom(1f, 2f, 3f); + Atom a2 = new Atom(7f, 6f, 5f); + Bond b = new Bond(a1, a2); + b.translate(8f, 9f, 10f); + assertEquals(9f, b.start[0], 0.0001f); + assertEquals(11f, b.start[1], 0.0001f); + assertEquals(13f, b.start[2], 0.0001f); + assertEquals(15f, b.end[0], 0.0001f); + assertEquals(15f, b.end[1], 0.0001f); + assertEquals(15f, b.end[2], 0.0001f); + } +} diff --git a/test/MCview/PDBChainTest.java b/test/MCview/PDBChainTest.java new file mode 100644 index 0000000..5be43b3 --- /dev/null +++ b/test/MCview/PDBChainTest.java @@ -0,0 +1,393 @@ +package MCview; + +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertFalse; +import static org.junit.Assert.assertSame; +import static org.junit.Assert.assertTrue; + +import java.awt.Color; +import java.util.Vector; + +import org.junit.Test; + +import jalview.analysis.AlignSeq; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.TaylorColourScheme; + +public class PDBChainTest +{ + PDBChain c = new PDBChain("1GAQ", "A"); + Atom a1 = new Atom(1f, 2f, 3f); + + Atom a2 = new Atom(5f, 6f, 4f); + + Atom a3 = new Atom(2f, 5f, 6f); + + Atom a4 = new Atom(2f, 1f, 7f); + + @Test + public void testGetNewlineString() + { + assertEquals(System.lineSeparator(), c.getNewlineString()); + c.setNewlineString("gaga"); + assertEquals("gaga", c.getNewlineString()); + } + + @Test + public void testPrint() + { + c.offset = 7; + + a1.resName = "GLY"; + a1.resNumber = 23; + a2.resName = "GLU"; + a2.resNumber = 34; + a3.resName = "ASP"; + a3.resNumber = 41; + + Vector v = new Vector(); + v.add(new Bond(a1, a2)); + v.add(new Bond(a2, a3)); + v.add(new Bond(a3, a1)); + c.bonds = v; + + String printed = c.print(); + String nl = System.lineSeparator(); + assertEquals("GLY 23 7" + nl + "GLU 34 7" + nl + "ASP 41 7" + nl, + printed); + } + + /** + * Test the method that constructs a Bond between two atoms and adds it to the + * chain's list of bonds + */ + @Test + public void testMakeBond() + { + /* + * Add a bond from a1 to a2 + */ + c.makeBond(a1, a2); + assertEquals(1, c.bonds.size()); + Bond b1 = c.bonds.get(0); + assertSame(a1, b1.at1); + assertSame(a2, b1.at2); + assertEquals(1f, b1.start[0], 0.0001f); + assertEquals(2f, b1.start[1], 0.0001f); + assertEquals(3f, b1.start[2], 0.0001f); + assertEquals(5f, b1.end[0], 0.0001f); + assertEquals(6f, b1.end[1], 0.0001f); + assertEquals(4f, b1.end[2], 0.0001f); + + /* + * Add another bond from a2 to a1 + */ + c.makeBond(a2, a1); + assertEquals(2, c.bonds.size()); + assertSame(b1, c.bonds.get(0)); + Bond b2 = c.bonds.get(1); + assertSame(a2, b2.at1); + assertSame(a1, b2.at2); + assertEquals(5f, b2.start[0], 0.0001f); + assertEquals(6f, b2.start[1], 0.0001f); + assertEquals(4f, b2.start[2], 0.0001f); + assertEquals(1f, b2.end[0], 0.0001f); + assertEquals(2f, b2.end[1], 0.0001f); + assertEquals(3f, b2.end[2], 0.0001f); + } + + @Test + public void testSetChainColours_colour() + { + c.makeBond(a1, a2); + c.makeBond(a2, a3); + c.setChainColours(Color.PINK); + assertEquals(2, c.bonds.size()); + assertEquals(Color.PINK, c.bonds.get(0).startCol); + assertEquals(Color.PINK, c.bonds.get(0).endCol); + assertEquals(Color.PINK, c.bonds.get(1).startCol); + assertEquals(Color.PINK, c.bonds.get(1).endCol); + } + + /** + * Test setting bond start/end colours based on a colour scheme i.e. colour by + * residue + */ + @Test + public void testSetChainColours_colourScheme() + { + Color alaColour = new Color(204, 255, 0); + Color glyColour = new Color(255, 153, 0); + a1.resName = "ALA"; + a2.resName = "GLY"; + a3.resName = "XXX"; // no colour defined + c.makeBond(a1, a2); + c.makeBond(a2, a1); + c.makeBond(a2, a3); + ColourSchemeI cs = new TaylorColourScheme(); + c.setChainColours(cs); + // bond a1 to a2 + Bond b = c.bonds.get(0); + assertEquals(alaColour, b.startCol); + assertEquals(glyColour, b.endCol); + // bond a2 to a1 + b = c.bonds.get(1); + assertEquals(glyColour, b.startCol); + assertEquals(alaColour, b.endCol); + // bond a2 to a3 - no colour found for a3 + // exception handling defaults to gray + b = c.bonds.get(2); + assertEquals(Color.gray, b.startCol); + assertEquals(Color.gray, b.endCol); + } + + @Test + public void testGetChargeColour() + { + assertEquals(Color.red, PDBChain.getChargeColour("ASP")); + assertEquals(Color.red, PDBChain.getChargeColour("GLU")); + assertEquals(Color.blue, PDBChain.getChargeColour("LYS")); + assertEquals(Color.blue, PDBChain.getChargeColour("ARG")); + assertEquals(Color.yellow, PDBChain.getChargeColour("CYS")); + assertEquals(Color.lightGray, PDBChain.getChargeColour("ALA")); + assertEquals(Color.lightGray, PDBChain.getChargeColour(null)); + } + + /** + * Test the method that sets bond start/end colours by residue charge property + */ + @Test + public void testSetChargeColours() + { + a1.resName = "ASP"; // red + a2.resName = "LYS"; // blue + a3.resName = "CYS"; // yellow + a4.resName = "ALA"; // no colour (light gray) + c.makeBond(a1, a2); + c.makeBond(a2, a3); + c.makeBond(a3, a4); + c.setChargeColours(); + assertEquals(3, c.bonds.size()); + // bond a1 to a2 + Bond b = c.bonds.get(0); + assertEquals(Color.red, b.startCol); + assertEquals(Color.blue, b.endCol); + // bond a2 to a3 + b = c.bonds.get(1); + assertEquals(Color.blue, b.startCol); + assertEquals(Color.yellow, b.endCol); + // bond a3 to a4 + b = c.bonds.get(2); + assertEquals(Color.yellow, b.startCol); + assertEquals(Color.lightGray, b.endCol); + } + + /** + * Test the method that converts the raw list of atoms to a list of residues + */ + @Test + public void testMakeResidueList_noAnnotation() + { + Vector atoms = new Vector(); + c.atoms = atoms; + c.isNa = true; + atoms.add(makeAtom(4, "N", "MET")); + atoms.add(makeAtom(4, "CA", "MET")); + atoms.add(makeAtom(4, "C", "MET")); + atoms.add(makeAtom(5, "O", "LYS")); + atoms.add(makeAtom(5, "N", "LYS")); + atoms.add(makeAtom(5, "CA", "LYS")); + atoms.add(makeAtom(6, "O", "LEU")); + atoms.add(makeAtom(6, "N", "LEU")); + atoms.add(makeAtom(6, "CA", "LEU")); + + c.makeResidueList(false); + + /* + * check sequence constructed + */ + assertEquals("MKL", c.sequence.getSequenceAsString()); + assertFalse(c.isNa); + assertEquals(3, c.residues.size()); + + /* + * check sequence features + */ + SequenceFeature[] sfs = c.sequence.getSequenceFeatures(); + assertEquals(3, sfs.length); + assertEquals("RESNUM", sfs[0].type); + assertEquals("MET:4 1gaqA", sfs[0].description); + assertEquals(4, sfs[0].begin); + assertEquals(4, sfs[0].end); + assertEquals("RESNUM", sfs[0].type); + assertEquals("LYS:5 1gaqA", sfs[1].description); + assertEquals(5, sfs[1].begin); + assertEquals(5, sfs[1].end); + assertEquals("LEU:6 1gaqA", sfs[2].description); + assertEquals(6, sfs[2].begin); + assertEquals(6, sfs[2].end); + } + + private Atom makeAtom(int resnum, String name, String resname) + { + Atom a = new Atom(1f, 2f, 3f); + a.resNumber = resnum; + a.resNumIns = String.valueOf(resnum); + a.name = name; + a.resName = resname; + a.chain = "A"; + return a; + } + + /** + * Test the method that converts the raw list of atoms to a list of residues, + * including parsing of tempFactor to an alignment annotation + */ + @Test + public void testMakeResidueList_withTempFactor() + { + Vector atoms = new Vector(); + c.atoms = atoms; + atoms.add(makeAtom(4, "N", "MET")); + atoms.get(atoms.size()-1).tfactor = 1f; + atoms.add(makeAtom(4, "CA", "MET")); + atoms.get(atoms.size()-1).tfactor = 2f; + atoms.add(makeAtom(4, "C", "MET")); + atoms.get(atoms.size()-1).tfactor = 3f; + atoms.add(makeAtom(5, "O", "LYS")); + atoms.get(atoms.size()-1).tfactor = 7f; + atoms.add(makeAtom(5, "N", "LYS")); + atoms.get(atoms.size()-1).tfactor = 8f; + atoms.add(makeAtom(5, "CA", "LYS")); + atoms.get(atoms.size()-1).tfactor = 9f; + atoms.add(makeAtom(6, "O", "LEU")); + atoms.get(atoms.size()-1).tfactor = 4f; + atoms.add(makeAtom(6, "N", "LEU")); + atoms.get(atoms.size()-1).tfactor = 5f; + atoms.add(makeAtom(6, "CA", "LEU")); + atoms.get(atoms.size()-1).tfactor = 6f; + + /* + * make residues including temp factor annotation + */ + c.makeResidueList(true); + + /* + * Verify annotations; note the tempFactor is read from the first atom in + * each residue i.e. we expect values 1, 7, 4 for the residues + */ + AlignmentAnnotation[] ann = c.sequence.getAnnotation(); + assertEquals(1, ann.length); + assertEquals("Temperature Factor", ann[0].label); + assertEquals("Temperature Factor for 1gaqA", ann[0].description); + assertSame(c.sequence, ann[0].sequenceRef); + assertEquals(AlignmentAnnotation.LINE_GRAPH, ann[0].graph); + assertEquals(0f, ann[0].graphMin, 0.001f); + assertEquals(7f, ann[0].graphMax, 0.001f); + assertEquals(3, ann[0].annotations.length); + assertEquals(1f, ann[0].annotations[0].value, 0.001f); + assertEquals(7f, ann[0].annotations[1].value, 0.001f); + assertEquals(4f, ann[0].annotations[2].value, 0.001f); + } + + /** + * Test the method that constructs bonds between successive residues' CA or P + * atoms + */ + @Test + public void testMakeCaBondList() + { + c.isNa = true; + Vector atoms = new Vector(); + c.atoms = atoms; + atoms.add(makeAtom(4, "N", "MET")); + atoms.add(makeAtom(4, "CA", "MET")); + atoms.add(makeAtom(5, "CA", "ASP")); + atoms.add(makeAtom(5, "O", "ASP")); + atoms.add(makeAtom(6, "CA", "GLY")); + atoms.add(makeAtom(6, "N", "GLY")); + + // have to make residue list first! + c.makeResidueList(false); + assertFalse(c.isNa); + c.isNa = true; + + c.makeCaBondList(); + assertEquals(2, c.bonds.size()); + Bond b = c.bonds.get(0); + assertSame(c.atoms.get(1), b.at1); + assertSame(c.atoms.get(2), b.at2); + b = c.bonds.get(1); + assertSame(c.atoms.get(2), b.at1); + assertSame(c.atoms.get(4), b.at2); + + // isNa flag is _not_ reset by this method! + assertTrue(c.isNa); + } + + @Test + public void testMakeCaBondList_nucleotide() + { + c.isNa = false; + Vector atoms = new Vector(); + c.atoms = atoms; + atoms.add(makeAtom(4, "N", "G")); + atoms.add(makeAtom(4, "P", "G")); + atoms.add(makeAtom(5, "P", "C")); + atoms.add(makeAtom(5, "O", "C")); + atoms.add(makeAtom(6, "P", "T")); + atoms.add(makeAtom(6, "N", "T")); + + // have to make residue list first! + c.makeResidueList(false); + assertEquals("GCT", c.sequence.getSequenceAsString()); + + c.makeCaBondList(); + assertEquals(2, c.bonds.size()); + Bond b = c.bonds.get(0); + assertSame(c.atoms.get(1), b.at1); + assertSame(c.atoms.get(2), b.at2); + b = c.bonds.get(1); + assertSame(c.atoms.get(2), b.at1); + assertSame(c.atoms.get(4), b.at2); + + assertTrue(c.isNa); + } + + /** + * Test the method that updates atoms with their alignment positions + */ + @Test + public void testMakeExactMapping() + { + Vector atoms = new Vector(); + c.atoms = atoms; + atoms.add(makeAtom(4, "N", "MET")); + atoms.add(makeAtom(4, "CA", "MET")); + atoms.add(makeAtom(5, "CA", "ASP")); + atoms.add(makeAtom(5, "O", "ASP")); + atoms.add(makeAtom(6, "CA", "GLY")); + atoms.add(makeAtom(6, "N", "GLY")); + c.makeResidueList(false); + assertEquals("MDG", c.sequence.getSequenceAsString()); + SequenceI s1 = new Sequence("Seq1", "MDG"); + SequenceI s2 = new Sequence("Seq2", "MDG"); + AlignSeq alignSeq = AlignSeq.doGlobalNWAlignment(s1, s2, AlignSeq.PEP); + SequenceI seq3 = new Sequence("Seq3", "--M-DG"); + c.makeExactMapping(alignSeq, seq3); + + int pos = 0; + for (Residue res : c.residues) + { + for (Atom a : res.atoms) + { + assertEquals(pos, a.alignmentMapping); + } + pos++; + } + } +} diff --git a/test/MCview/PDBfileTest.java b/test/MCview/PDBfileTest.java new file mode 100644 index 0000000..9ebed25 --- /dev/null +++ b/test/MCview/PDBfileTest.java @@ -0,0 +1,272 @@ +package MCview; + +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertFalse; +import static org.junit.Assert.assertNull; +import static org.junit.Assert.assertSame; +import static org.junit.Assert.assertTrue; + +import java.io.IOException; + +import org.junit.Ignore; +import org.junit.Test; + +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceI; +import jalview.io.AppletFormatAdapter; + +public class PDBfileTest +{ + @Test + public void testIsRna() + { + SequenceI seq = new Sequence("Seq1", "CGAU"); + assertTrue(PDBfile.isRNA(seq)); + + seq.setSequence("CGAu"); + assertFalse(PDBfile.isRNA(seq)); + + seq.setSequence("CGAT"); + assertFalse(PDBfile.isRNA(seq)); + + seq.setSequence("GRSWYFLAVM"); + assertFalse(PDBfile.isRNA(seq)); + } + + /** + * Test the 'high level' outputs of parsing. More detailed tests in + * PDBChainTest. + * + * @throws IOException + */ + @Test + public void testParse() throws IOException + { + /* + * Constructor with file path performs parse() + */ + PDBfile pf = new PDBfile(false, false, false, "examples/3W5V.pdb", + AppletFormatAdapter.FILE); + + assertEquals("3W5V", pf.id); + // verify no alignment annotations created + assertNull(getAlignmentAnnotations(pf)); + + assertEquals(4, pf.chains.size()); + assertEquals("A", pf.chains.get(0).id); + assertEquals("B", pf.chains.get(1).id); + assertEquals("C", pf.chains.get(2).id); + assertEquals("D", pf.chains.get(3).id); + + PDBChain chainA = pf.chains.get(0); + assertEquals(0, chainA.seqstart); // not set + assertEquals(0, chainA.seqend); // not set + assertEquals(18, chainA.sequence.getStart()); + assertEquals(314, chainA.sequence.getEnd()); + assertTrue(chainA.sequence.getSequenceAsString().startsWith("KCSKKQEE")); + assertTrue(chainA.sequence.getSequenceAsString().endsWith("WNVEVY")); + assertEquals("3W5V|A", chainA.sequence.getName()); + assertNull(chainA.sequence.getAnnotation()); + assertEquals(1, chainA.sequence.getPDBId().size()); + PDBEntry pdb = chainA.sequence.getPDBId().get(0); + assertEquals("A", pdb.getChainCode()); + assertEquals("PDB", pdb.getType()); + assertEquals("3W5V", pdb.getId()); + + PDBChain chainB = pf.chains.get(1); + assertEquals(1, chainB.sequence.getStart()); + assertEquals(96, chainB.sequence.getEnd()); + assertTrue(chainB.sequence.getSequenceAsString().startsWith("ATYNVK")); + assertTrue(chainB.sequence.getSequenceAsString().endsWith("KEEELT")); + assertEquals("3W5V|B", chainB.sequence.getName()); + + PDBChain chainC = pf.chains.get(2); + assertEquals(18, chainC.sequence.getStart()); + assertEquals(314, chainC.sequence.getEnd()); + assertTrue(chainC.sequence.getSequenceAsString().startsWith("KCSKKQEE")); + assertTrue(chainC.sequence.getSequenceAsString().endsWith("WNVEVY")); + assertEquals("3W5V|C", chainC.sequence.getName()); + + PDBChain chainD = pf.chains.get(3); + assertEquals(1, chainD.sequence.getStart()); + assertEquals(96, chainD.sequence.getEnd()); + assertTrue(chainD.sequence.getSequenceAsString().startsWith("ATYNVK")); + assertTrue(chainD.sequence.getSequenceAsString().endsWith("KEEELT")); + assertEquals("3W5V|D", chainD.sequence.getName()); + } + + /** + * Test parsing, with annotations added to the alignment but no secondary + * structure prediction + * + * @throws IOException + */ + @Test + public void testParse_withAnnotations_noSS() throws IOException + { + PDBfile pf = new PDBfile(true, false, false, "examples/3W5V.pdb", + AppletFormatAdapter.FILE); + + AlignmentAnnotation[] anns = getAlignmentAnnotations(pf); + assertEquals(4, anns.length); + + /* + * Inspect temp factor annotation for chain A + */ + AlignmentAnnotation chainAnnotation = anns[0]; + assertEquals("Temperature Factor", chainAnnotation.label); + // PDBChain constructor changes PDB id to lower case (why?) + assertEquals("Temperature Factor for 3w5vA", + chainAnnotation.description); + assertSame(pf.getSeqs().get(0), chainAnnotation.sequenceRef); + assertEquals(AlignmentAnnotation.LINE_GRAPH, chainAnnotation.graph); + assertEquals(0f, chainAnnotation.graphMin, 0.001f); + assertEquals(40f, chainAnnotation.graphMax, 0.001f); + assertEquals(297, chainAnnotation.annotations.length); + assertEquals(40f, chainAnnotation.annotations[0].value, 0.001f); + + /* + * Chain B temp factor + */ + chainAnnotation = anns[1]; + assertEquals("Temperature Factor for 3w5vB", + chainAnnotation.description); + assertSame(pf.getSeqs().get(1), chainAnnotation.sequenceRef); + assertEquals(96, chainAnnotation.annotations.length); + + /* + * Chain C temp factor + */ + chainAnnotation = anns[2]; + assertEquals("Temperature Factor for 3w5vC", + chainAnnotation.description); + assertSame(pf.getSeqs().get(2), chainAnnotation.sequenceRef); + assertEquals(297, chainAnnotation.annotations.length); + + /* + * Chain D temp factor + */ + chainAnnotation = anns[3]; + assertEquals("Temperature Factor for 3w5vD", + chainAnnotation.description); + assertSame(pf.getSeqs().get(3), chainAnnotation.sequenceRef); + assertEquals(96, chainAnnotation.annotations.length); + } + + /** + * Test parsing including secondary structure annotation using JMol; this test + * for the case where flag to add annotations to alignment is set false + * + * @throws IOException + */ + @Test + public void testParse_withJmol_noAnnotations() throws IOException + { + PDBfile pf = new PDBfile(false, true, false, "examples/3W5V.pdb", + AppletFormatAdapter.FILE); + + /* + * alignment annotations _are_ created anyway (in + * AlignSeq.replaceMatchingSeqsWith()) + */ + final AlignmentAnnotation[] anns = getAlignmentAnnotations(pf); + assertEquals(4, anns.length); + + /* + * no sequence annotations created - tempFactor annotation is not added + * unless the flag to 'addAlignmentAnnotations' is set true + */ + for (PDBChain c : pf.chains) + { + assertNull(c.sequence.getAnnotation()); + } + } + + /** + * Test parsing including secondary structure prediction and annotation using + * JMol + * + * @throws IOException + */ + @Test + public void testParse_withJmolAddAlignmentAnnotations() + throws IOException + { + PDBfile pf = new PDBfile(true, true, false, "examples/3W5V.pdb", + AppletFormatAdapter.FILE); + + /* + * Alignment annotations for TempFactor, SecStruct, per sequence (chain) + */ + AlignmentAnnotation[] anns = getAlignmentAnnotations(pf); + assertEquals(8, anns.length); + + /* + * other tests have detailed assertions for Temp Factor annotations + */ + assertEquals("Temperature Factor for 3w5vA", anns[1].description); + assertEquals("Temperature Factor for 3w5vB", anns[3].description); + assertEquals("Temperature Factor for 3w5vC", anns[5].description); + assertEquals("Temperature Factor for 3w5vD", anns[7].description); + + /* + * PDBFileWithJmol (unlike PDBChain!) leaves PDB id upper case + */ + assertEquals("Secondary Structure for 3W5VA", anns[0].description); + assertEquals("Secondary Structure for 3W5VB", anns[2].description); + assertEquals("Secondary Structure for 3W5VC", anns[4].description); + assertEquals("Secondary Structure for 3W5VD", anns[6].description); + + /* + * Verify SS annotations are linked to respective sequences (chains) + */ + assertSame(pf.getSeqs().get(0), anns[0].sequenceRef); + assertSame(pf.getSeqs().get(1), anns[2].sequenceRef); + assertSame(pf.getSeqs().get(2), anns[4].sequenceRef); + assertSame(pf.getSeqs().get(3), anns[6].sequenceRef); + + /* + * Verify a sample of SS predictions + */ + for (int i = 0; i < 20; i++) + { + assertNull(anns[0].annotations[i]); + assertEquals("E", anns[0].annotations[20].displayCharacter); + assertEquals('E', anns[0].annotations[20].secondaryStructure); + assertEquals("E", anns[2].annotations[18].displayCharacter); + assertEquals("H", anns[2].annotations[23].displayCharacter); + } + } + + /** + * Placeholder for a test of parsing RNA structure with secondary structure + * prediction using the Annotate3D service + * + * @throws IOException + */ + @Test + @Ignore + public void testParse_withAnnotate3D() throws IOException + { + // TODO requires a mock for Annotate3D processing + // and/or run as an integration test + PDBfile pf = new PDBfile(true, true, true, "examples/2GIS.pdb", + AppletFormatAdapter.FILE); + } + /** + * Helper method to extract parsed annotations from the PDBfile + * + * @param pf + * @return + */ + private AlignmentAnnotation[] getAlignmentAnnotations(PDBfile pf) + { + AlignmentI al = new Alignment(pf.getSeqsAsArray()); + pf.addAnnotations(al); + return al.getAlignmentAnnotation(); + } + } diff --git a/test/MCview/ResidueTest.java b/test/MCview/ResidueTest.java new file mode 100644 index 0000000..ed98c5b --- /dev/null +++ b/test/MCview/ResidueTest.java @@ -0,0 +1,36 @@ +package MCview; + +import static org.junit.Assert.assertNull; +import static org.junit.Assert.assertSame; + +import java.util.Vector; + +import org.junit.Test; + +public class ResidueTest +{ + + @Test + public void testFindAtom() + { + Atom a1 = new Atom(1f, 2f, 3f); + a1.name = "C"; + Atom a2 = new Atom(1f, 2f, 3f); + a2.name = "A"; + Atom a3 = new Atom(1f, 2f, 3f); + a3.name = "P"; + Atom a4 = new Atom(1f, 2f, 3f); + a4.name = "C"; + Vector v = new Vector(); + v.add(a1); + v.add(a2); + v.add(a3); + v.add(a4); + Residue r = new Residue(v, 293, 12); + + assertSame(a1, r.findAtom("C")); + assertSame(a2, r.findAtom("A")); + assertSame(a3, r.findAtom("P")); + assertNull(r.findAtom("S")); + } +} -- 1.7.10.2