Mini-Retreat Two

Logistics

Topics for Discussion

Agenda

Friday

9:15AM - 6:00PM

(Note: ISB group can't stay for Saturday, need view model nailed down and some talk about the web stuff)

Saturday

9:30AM - 3:00PM

Goal

Pre-meeting Comments

Decisions and Results

This is an attempt pull together the major decisions we made and (possibly) the areas where we might need further discussion (perhaps via E-Mail).

Architecture

Model

View Model

Presentation

Events

Model

View Model

VizMap Events

Presentation Events

Meeting Notes

Day 1

Review of architecture: (photo will be attached)

Examples:

Questions:

VizMap:

Web presentation strategy:

Presentation Layer:

Summary:

Tomorrow:

Day 2

While listing events below, we realized that we really need a Presentation and ViewModel for CyDataTable. This will support events in the Table, all the same events needed for Network. With proper View Model support, this doesn't even have to be table! This could be histograms and heatmaps.

Presentation Events:

View Model Events (again, for both Networks and CyDataTables):

VizMap Events:

Model Events:

Need for an Action-Event Broker:

Idea for Decorations:

Event-coalescence optimization [:Cytoscape_3.0/MiniRetreatTwo/DanielsQuestions#head-4b142dfa6d192e4392845c4904639ac51b601b6c: Daniels Starter Questions]

Batchable.java 

interface Batchable {
        void batchBegin();
        void batchEnd();
}

NetworkThingy.java 

import java.util.ArrayList;
import java.util.List;

class NetworkThingy implements Batchable {
        boolean inBatch = false;
        List<String> addEventList = null;
        List<String> removeEventList = null;

        public NetworkThingy () {}

        public void addNetworkSubThingy (String name) {
                if (!inBatch)
                        System.out.println("Added network sub-thingy "+name);
                else
                        addEvent(name);
        }

        public void deleteNetworkSubThingy (String name) {
                if (!inBatch)
                        System.out.println("Deleted network sub-thingy "+name);
                else
                        removeEvent(name);
        }

        public void batchBegin() {
                inBatch = true;
        }

        public void batchEnd() {
                inBatch = false;
                if (addEventList != null && addEventList.size() > 0) {
                        System.out.print("Added sub-thingy's ");
                        for (String event: addEventList) {
                                System.out.print(event+", ");
                        }
                        System.out.println();
                }

                if (removeEventList != null && removeEventList.size() > 0) {
                        System.out.print("Removed sub-thingy's ");
                        for (String event: removeEventList) {
                                System.out.print(event+", ");
                        }
                        System.out.println();
                }

                addEventList = null;
                removeEventList = null;
        }

        private void addEvent(String name) {
                if (addEventList == null)
                        addEventList = new ArrayList();

                addEventList.add(name);
        }

        private void removeEvent(String name) {
                if (addEventList != null && addEventList.contains(name)) {
                        addEventList.remove(name);
                        return;
                }

                if (removeEventList == null)
                        removeEventList = new ArrayList();

                removeEventList.add(name);
        }
}

TestBatch.java 

public class TestBatch {

        public static void main(String[] args) {
                NetworkThingy thingy = new NetworkThingy();

                for (int i = 0; i < 100; i++) {
                        thingy.addNetworkSubThingy("ST "+i);
                }

                thingy.batchBegin();
                for (int i = 0; i < 100; i++) {
                        thingy.addNetworkSubThingy("ST "+(i+100));
                }
                thingy.batchEnd();

                thingy = new NetworkThingy();
                thingy.batchBegin();
                for (int i = 0; i < 100; i++) {
                        thingy.addNetworkSubThingy("ST "+i);
                }

                thingy.deleteNetworkSubThingy("ST 5");
                thingy.deleteNetworkSubThingy("ST 50");
                thingy.batchEnd();

        }
}

Work Layer:

I/O Layer:

CyReaderManager:

CyReader:

When is the ViewModel built?

Summary:

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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