biojava · lafita · Jun 16, 2015 · Apr 20, 2015 · Apr 22, 2015 · Apr 22, 2015
diff --git a/biojava-structure-gui/src/main/java/demo/CookBook.java b/biojava-structure-gui/src/main/java/demo/CookBook.java
@@ -91,7 +91,7 @@ public static void main(String[] args){
          jmol.setTitle(algorithm.getAlgorithmName() + " : " + name1 + " vs. " + name2);
 
          // here we open up the alignment - text panel that can interact with the 3D jmol display.
-         DisplayAFP.showAlignmentImage(afpChain, ca1,ca2,jmol);
+         DisplayAFP.showAlignmentPanel(afpChain, ca1,ca2,jmol);
 
          // we can print an XML version 
          //System.out.println(AFPChainXMLConverter.toXML(afpChain, ca1, ca2));

diff --git a/biojava-structure-gui/src/main/java/demo/DemoCEMC.java b/biojava-structure-gui/src/main/java/demo/DemoCEMC.java
@@ -0,0 +1,70 @@
+package demo;
+
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.List;
+import java.util.ArrayList;
+import java.util.concurrent.ExecutionException;
+
+import org.biojava.nbio.structure.Atom;
+import org.biojava.nbio.structure.StructureException;
+import org.biojava.nbio.structure.align.cemc.CeMcMain;
+import org.biojava.nbio.structure.align.gui.MultipleAlignmentDisplay;
+import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
+import org.biojava.nbio.structure.align.util.AtomCache;
+
+/**
+ * Demo for running a CEMC Multiple Structure Alignment and visualizing the results.
+ * 
+ * @author Aleix Lafita
+ * 
+ */
+public class DemoCEMC {
+
+	public static void main(String[] args) throws IOException, StructureException, InterruptedException, ExecutionException {
+
+		//Specify the structures to align
+		//ASP-proteinases (CEMC paper)
+		//List<String> names = Arrays.asList("3app", "4ape", "2apr", "5pep", "1psn", "4cms", "1bbs.A", "1smr.A", "2jxr.A", "1mpp", "2asi", "1am5");
+		//Protein Kinases (CEMC paper)
+		//List<String> names = Arrays.asList("1cdk.A", "1cja.A", "1csn", "1b6c.B", "1ir3.A", "1fgk.A", "1byg.A", "1hck", "1blx.A", "3erk", "1bmk.A", "1kob.A", "1tki.A", "1phk", "1a06");
+		//DHFR (Gerstein 1998 paper)
+		List<String> names = Arrays.asList("d1dhfa_", "8dfr", "d4dfra_", "3dfr");
+		//TIM barrels (MUSTA paper)
+		//List<String> names = Arrays.asList("1tim.A", "1vzw", "1nsj", "3tha.A", "4enl", "2mnr", "7tim.A", "1tml", "1btc", "a1piia1", "6xia", "5rub.A", "2taa.B");
+		//Helix-bundle (MUSTA paper)
+		//List<String> names = Arrays.asList("1bbh.A", "1aep", "1bge.B", "256b.A", "2ccy.A", "2hmz.A", "3ink.C");
+		//Calcium Binding (MUSTA paper)
+		//List<String> names = Arrays.asList("4cpv", "2scp.A", "2sas", "1top", "1scm.B", "3icb");
+		//Serine Rich Proteins SERP (MUSTA paper)
+		//List<String> names = Arrays.asList("7api.A", "8api.A", "1hle.A", "1ova.A", "2ach.A", "9api.A", "1psi", "1atu", "1kct", "1ath.A", "1att.A");
+		//Serine Proteases (MUSTA paper)
+		//List<String> names = Arrays.asList("1cse.E", "1sbn.E", "1pek.E", "3prk", "3tec.E");
+		//GPCRs
+		//List<String> names = Arrays.asList("2z73.A", "1u19.A", "4ug2.A", "4xt3", "4or2.A", "3odu.A");
+		//Immunoglobulins (MAMMOTH paper)
+		//List<String> names = Arrays.asList("2hla.B", "3hla.B", "1cd8", "2rhe", "1tlk", "1ten", "1ttf");
+		//Globins (MAMMOTH and MUSTA papers)
+		//List<String> names = Arrays.asList("1mbc", "1hlb", "1thb.A", "1ith.A", "1idr.A", "1dlw", "1kr7.A", "1ew6.A", "1it2.A", "1eco", "3sdh.A", "1cg5.B", "1fhj.B", "1ird.A", "1mba", "2gdm", "1b0b", "1h97.A", "1ash.A", "1jl7.A");
+		//Rossman-Fold (POSA paper)
+		//List<String> names = Arrays.asList("d1heta2", "d1ek6a_", "d1obfo1", "2cmd", "d1np3a2", "d1bgva1", "d1id1a_", "d1id1a_", "d1oi7a1");
+
+		//Load the CA atoms of the structures
+		AtomCache cache = new AtomCache();
+		List<Atom[]> atomArrays = new ArrayList<Atom[]>();
+		for (String name:names)	{
+			atomArrays.add(cache.getAtoms(name));
+		}
+
+		//Here the multiple structural alignment algorithm comes in place to generate the alignment object
+		CeMcMain algorithm = new CeMcMain();
+		MultipleAlignment result = algorithm.align(atomArrays);
+		result.getEnsemble().setStructureNames(names);
+
+		//Information about the alignment
+		result.getEnsemble().setAlgorithmName(algorithm.getAlgorithmName());
+		result.getEnsemble().setVersion(algorithm.getVersion());
+
+		MultipleAlignmentDisplay.display(result);
+	}
+}
diff --git a/biojava-structure-gui/src/main/java/demo/DemoMultipleAlignmentJmol.java b/biojava-structure-gui/src/main/java/demo/DemoMultipleAlignmentJmol.java
@@ -0,0 +1,128 @@
+package demo;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.biojava.nbio.structure.Atom;
+import org.biojava.nbio.structure.StructureException;
+import org.biojava.nbio.structure.align.gui.MultipleAlignmentDisplay;
+import org.biojava.nbio.structure.align.multiple.Block;
+import org.biojava.nbio.structure.align.multiple.BlockImpl;
+import org.biojava.nbio.structure.align.multiple.BlockSet;
+import org.biojava.nbio.structure.align.multiple.BlockSetImpl;
+import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
+import org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble;
+import org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl;
+import org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl;
+import org.biojava.nbio.structure.align.multiple.MultipleAlignmentScorer;
+import org.biojava.nbio.structure.align.multiple.MultipleAlignmentWriter;
+import org.biojava.nbio.structure.align.multiple.MultipleSuperimposer;
+import org.biojava.nbio.structure.align.multiple.ReferenceSuperimposer;
+import org.biojava.nbio.structure.align.util.AtomCache;
+
+/**
+ * Demo for visualizing the results of a Multiple Alignment, from a sample MultipleAlignment object.
+ * 
+ * @author Aleix Lafita
+ * 
+ */
+public class DemoMultipleAlignmentJmol {
+
+	public static void main(String[] args) throws IOException, StructureException {
+
+		//Specify the structures to align
+		//List<String> names = Arrays.asList("1tim.a", "1vzw", "1nsj", "3tha.a");	//TIM barrels
+		List<String> names = Arrays.asList("1mbc", "1hlb", "1thb.a", "1ith.a");		//globins
+
+		//Load the CA atoms of the structures
+		AtomCache cache = new AtomCache();
+		List<Atom[]> atomArrays = new ArrayList<Atom[]>();
+		for (String name:names) atomArrays.add(cache.getAtoms(name));
+
+		//Here the multiple structural alignment algorithm comes in place to generate the alignment object
+		MultipleAlignment fakeMultAln = fakeMultipleAlignment("globins", atomArrays);
+		fakeMultAln.getEnsemble().setStructureNames(names);
+
+		//Generate a pairwise alignment and convert it to a MultipleAlignment
+		//FatCat fatcat  = new FatCat();
+		//AFPChain afpChain = fatcat.alignRigid(atomArrays.get(0),atomArrays.get(1));
+		//MultipleAlignmentEnsemble ensemble = new MultipleAlignmentEnsembleImpl(afpChain, atomArrays.get(0),atomArrays.get(1));
+		//MultipleAlignment pairwise = ensemble.getMultipleAlignments().get(0);
+
+		System.out.println(MultipleAlignmentWriter.toFASTA(fakeMultAln));
+		MultipleAlignmentDisplay.display(fakeMultAln);
+		//StructureAlignmentDisplay.display(pairwise);
+		//For comparison display the original AFP
+		//StructureAlignmentDisplay.display(afpChain,atomArrays.get(0),atomArrays.get(1));
+	}
+
+	/**
+	 * Method that constructs a fake MultipleAlignment with two BlockSets, with two and one Blocks respectively. Used to
+	 * test the correctness of the DataStructure. In the future it will be in the Test packages.
+	 * @param family name of the protein family
+	 * @param atomArrays
+	 * @return MultipleAlignment
+	 * @throws StructureException
+	 * @throws StructureAlignmentException
+	 */
+	private static MultipleAlignment fakeMultipleAlignment(String family, List<Atom[]>atomArrays) throws StructureException {
+
+		//Initialize the multiple alignment parent ensemble
+		MultipleAlignmentEnsemble ensemble = new MultipleAlignmentEnsembleImpl();
+		ensemble.setAtomArrays(atomArrays);
+		ensemble.setAlgorithmName("fakeAlgorithm");
+		MultipleAlignment fakeMultAln = new MultipleAlignmentImpl(ensemble);
+
+		if (family == "globins"){
+
+			BlockSet blockSet1 = new BlockSetImpl(fakeMultAln); //first BlockSet with 2 Blocks
+			BlockSet blockSet2 = new BlockSetImpl(fakeMultAln); //second BlockSet with 1 Block
+
+			Block block1 = new BlockImpl(blockSet1);
+			Block block2 = new BlockImpl(blockSet1);
+
+			Block block3 = new BlockImpl(blockSet2);
+
+			//Alignment obtained from MUSTANG multiple alignment (just some of the residues, not the whole alignment)
+			List<Integer> aligned11 = Arrays.asList(0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21);
+			List<Integer> aligned12 = Arrays.asList(29,30,31,32,33,34,35,36,38);
+			List<Integer> aligned13 = Arrays.asList(123,124,125,126,127,128,129,130,131,132,133,134);
+
+			List<Integer> aligned21 = Arrays.asList(10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,null,27,28,29,30,31);
+			List<Integer> aligned22 = Arrays.asList(39,40,41,42,43,44,45,46,48);
+			List<Integer> aligned23 = Arrays.asList(133,134,135,136,137,138,139,140,141,142,143,144);
+
+			List<Integer> aligned31 = Arrays.asList(0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21);
+			List<Integer> aligned32 = Arrays.asList(29,30,31,32,33,34,35,36,38);
+			List<Integer> aligned33 = Arrays.asList(117,118,119,120,121,122,123,124,125,126,127,128);
+
+			List<Integer> aligned41 = Arrays.asList(0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,null,17,18,19,20,21);
+			List<Integer> aligned42 = Arrays.asList(30,31,32,33,34,35,36,37,39);
+			List<Integer> aligned43 = Arrays.asList(121,122,123,124,125,126,127,128,129,130,131,132);
+
+			block1.getAlignRes().add(aligned11);
+			block1.getAlignRes().add(aligned21);
+			block1.getAlignRes().add(aligned31);
+			block1.getAlignRes().add(aligned41);
+
+			block2.getAlignRes().add(aligned12);
+			block2.getAlignRes().add(aligned22);
+			block2.getAlignRes().add(aligned32);
+			block2.getAlignRes().add(aligned42);
+
+			block3.getAlignRes().add(aligned13);
+			block3.getAlignRes().add(aligned23);
+			block3.getAlignRes().add(aligned33);
+			block3.getAlignRes().add(aligned43);
+
+			//Calculating all information in the alignment is as easy as that line, once the residue equivalencies are set
+			MultipleSuperimposer imposer = new ReferenceSuperimposer();
+			imposer.superimpose(fakeMultAln);
+			MultipleAlignmentScorer.calculateScores(fakeMultAln);
+		}
+		return fakeMultAln;
+	}
+
+}
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentCalc.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentCalc.java
@@ -106,14 +106,13 @@ public void run() {
 				title += " " + algorithm.getParameters().toString();
 			jmol.setTitle(title);
 
-			DisplayAFP.showAlignmentImage(afpChain,ca1,ca2,jmol);           
+			DisplayAFP.showAlignmentPanel(afpChain,ca1,ca2,jmol);
 
 			System.out.println(afpChain.toCE(ca1,ca2));
 
 		} catch (StructureException e){
 			e.printStackTrace();
 			logger.warn(e.getMessage());
-
 		}
 
 

diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DBResultTable.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DBResultTable.java
@@ -338,7 +338,7 @@ private void showAlignment( String name1, String name2){
 
 			//String rot = afpChain.toRotMat();
 
-			DisplayAFP.showAlignmentImage(afpChain, ca1,ca2,jmol);
+			DisplayAFP.showAlignmentPanel(afpChain, ca1,ca2,jmol);
 
 
 		} catch (Exception e){